mixmodel4repeated_measures: mixmodel

annotate mixmodel_script.R @ 0:a4d89d47646f draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8

author	workflow4metabolomics
date	Mon, 16 May 2022 09:25:01 +0000
parents
children

rev	line source
0 a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	1 ####### R functions to perform linear mixed model for repeated measures
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	2 ####### on a multi var dataset using 3 files as used in W4M
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	3 ##############################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	4 lmRepeated2FF <- function(ids, ifixfact, itime, isubject, ivd, ndim, nameVar=colnames(ids)[[ivd]],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	5 pvalCutof = 0.05, dffOption, visu = visu, tit = "", least.confounded = FALSE, outlier.limit = 3) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	6 ### function to perform linear mixed model with 1 Fixed factor + Time + random factor subject
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	7 ### based on lmerTest package providing functions giving the same results as SAS proc mixed
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	8 options(scipen = 50, digits = 5)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	9
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	10 if (!is.numeric(ids[[ivd]])) stop("Dependant variable is not numeric")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	11 if (!is.factor(ids[[ifixfact]])) stop("fixed factor is not a factor")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	12 if (!is.factor(ids[[itime]])) stop("Repeated factor is not a factor")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	13 if (!is.factor(ids[[isubject]])) stop("Random factor is not a factor")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	14
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	15 ## factors
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	16 time <- ids[[itime]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	17 fixfact <- ids[[ifixfact]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	18 subject <- ids[[isubject]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	19 # dependant variables
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	20 vd <- ids[[ivd]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	21
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	22 # argument of the function instead of re re-running ndim <- defColRes(ids, ifixfact, itime)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	23 # nfp : number of main factors + model infos (REML, varSubject) + normality test
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	24 nfp <- ndim[1];
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	25 # ncff number of comparison of the fixed factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	26 nlff <- ndim[2]; ncff <- ndim[3]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	27 # nct number of comparison of the time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	28 nlt <- ndim[4]; nct <- ndim[5]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	29 # nci number of comparison of the interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	30 nli <- ndim[6]; nci <- ndim[7]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	31 # number of all lmer results
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	32 nresT <- ncff + nct + nci
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	33 ## initialization of the result vector (1 line)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	34 ## 4 * because nresf for : pvalues + Etimates + lower CI + Upper CI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	35 res <- data.frame(array(rep(NA, (nfp + 4 * nresT))))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	36 colnames(res)[1] <- "resultLM"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	37
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	38 ### if at least one subject have data for only 1 time, mixed model is not possible and variable must be skip
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	39 ### after excluding NA, table function is used to seek subjects with only 1 data
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	40 ids <- ids[!is.na(ids[[ivd]]), ]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	41 skip <- length(which(table(ids[[isubject]]) == 1))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	42
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	43 if (skip == 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	44
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	45 mfl <- lmer(vd ~ time + fixfact + time:fixfact + (1 \| subject), ids) # lmer remix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	46
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	47 rsum <- summary(mfl, ddf = dffOption)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	48 ## test Shapiro Wilks on the residus of the model
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	49 rShapiro <- shapiro.test(rsum$residuals)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	50 raov <- anova(mfl, ddf = dffOption)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	51 dlsm1 <- data.frame(difflsmeans(mfl, test.effs = NULL))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	52 ddlsm1 <- dlsm1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	53 ## save rownames and factor names
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	54 rn <- rownames(ddlsm1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	55 fn <- ddlsm1[, c(1, 2)]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	56 ## writing the results on a single line
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	57 namesFactEstim <- paste("estimate ", rownames(ddlsm1)[c(1:(nct + ncff))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	58 namesFactPval <- paste("pvalue ", rownames(ddlsm1)[c(1:(nct + ncff))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	59 namesInter <- rownames(ddlsm1)[-c(1:(nct + ncff))]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	60 namesEstimate <- paste("estimate ", namesInter)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	61 namespvalues <- paste("pvalue ", namesInter)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	62 namesFactprinc <- c("pval_time", "pval_trt", "pval_inter")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	63 namesFactEstim <- paste("estimate ", rownames(ddlsm1)[c(1:(nct + ncff))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	64
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	65 namesFactLowerCI <- paste("lowerCI ", rownames(ddlsm1)[c(1:(nct + ncff))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	66 namesLowerCI <- paste("lowerCI ", namesInter, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	67
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	68 namesFactUpperCI <- paste("UpperCI ", rownames(ddlsm1)[c(1:(nct + ncff))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	69 namesUpperCI <- paste("UpperCI ", namesInter, sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	70
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	71
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	72 ### lmer results on 1 vector row
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	73 # pvalue of shapiro Wilks test of the residuals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	74 res[1, ] <- rShapiro$p.value; rownames(res)[1] <- "Shapiro.pvalue.residuals"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	75 res[2, ] <- rsum$varcor$subject[1] ;rownames(res)[2] <- "Subject.Variance"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	76 res[3, ] <- rsum$devcomp$cmp[7] ; rownames(res)[3] <- "REML"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	77 ### 3 principal factors pvalues results + shapiro test => nfp <- 4
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	78 res[c((nfp - 2):nfp), ] <- raov[, 6]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	79 rownames(res)[c((nfp - 2):nfp)] <- namesFactprinc
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	80
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	81 #################### Residuals diagnostics for significants variables #########################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	82 ### Il at least 1 factor is significant and visu=TRUE NL graphics add to pdf
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	83 ## ajout JF du passage de la valeur de p-value cutoff
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	84 if (length(which(raov[, 6] <= pvalCutof)) > 0 & visu == "yes") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	85 diagmflF(mfl, title = tit, pvalCutof = pvalCutof, least.confounded = least.confounded,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	86 outlier.limit = outlier.limit)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	87 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	88
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	89 # pvalue of fixed factor comparisons
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	90 nresf <- nresT
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	91 res[(nfp + 1):(nfp + nct), ] <- ddlsm1[c(1:nct), 9]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	92 res[(nfp + nct + 1):(nfp + nct + ncff), ] <- ddlsm1[(nct + 1):(nct + ncff), 9]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	93 rownames(res)[(nfp + 1):(nfp + nct + ncff)] <- namesFactPval
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	94 res[(nfp + nct + ncff + 1):(nfp + nresf), ] <- ddlsm1[(nct + ncff + 1):(nresT), 9]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	95 rownames(res)[(nfp + nct + ncff + 1):(nfp + nresT)] <- namespvalues
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	96 # Estimate of the difference between levels of factors
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	97 res[(nfp + nresf + 1):(nfp + nresf + nct), ] <- ddlsm1[c(1:nct), 3]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	98 res[(nfp + nresf + nct + 1):(nfp + nresf + nct + ncff), ] <- ddlsm1[(nct + 1):(nct + ncff), 3]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	99 rownames(res)[(nfp + nresf + 1):(nfp + nresf + nct + ncff)] <- namesFactEstim
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	100 res[(nfp + nresf + nct + ncff + 1):(nfp + 2 * nresf), ] <- ddlsm1[(nct + ncff + 1):(nresT), 3]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	101 rownames(res)[(nfp + nresf + nct + ncff + 1):(nfp + 2 * nresf)] <- namesEstimate
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	102 # lower CI of the difference between levels of factors
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	103 nresf <- nresf + nresT
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	104 res[(nfp + nresf + 1):(nfp + nresf + nct), ] <- ddlsm1[c(1:nct), 7]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	105 res[(nfp + nresf + nct + 1):(nfp + nresf + nct + ncff), ] <- ddlsm1[(nct + 1):(nct + ncff), 7]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	106 rownames(res)[(nfp + nresf + 1):(nfp + nresf + nct + ncff)] <- namesFactLowerCI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	107 res[(nfp + nresf + nct + ncff + 1):(nfp + 2 * nresf), ] <- ddlsm1[(nct + ncff + 1):(nresf), 7]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	108 rownames(res)[(nfp + nresf + nct + ncff + 1):(nfp + nresf + (nresf / 2))] <- namesLowerCI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	109 # Upper CI of the difference between levels of factors
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	110 nresf <- nresf + nresT
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	111 res[(nfp + nresf + 1):(nfp + nresf + nct), ] <- ddlsm1[c(1:nct), 8]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	112 res[(nfp + nresf + nct + 1):(nfp + nresf + nct + ncff), ] <- ddlsm1[(nct + 1):(nct + ncff), 8]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	113 rownames(res)[(nfp + nresf + 1):(nfp + nresf + nct + ncff)] <- namesFactUpperCI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	114 res[(nfp + nresf + nct + ncff + 1):(nfp + nresf + (nresT)), ] <- ddlsm1[(nct + ncff + 1):(nresT), 8]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	115 rownames(res)[(nfp + nresf + nct + ncff + 1):(nfp + nresf + (nresT))] <- namesUpperCI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	116
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	117 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	118 ## one of the subject has only one time, subject can't be a random variable
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	119 ## A repeated measure could be run instead function lme of package nlme, in next version?
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	120 res[1, ] <- NA
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	121 cat("\n Computing impossible for feature ", tit, ": at least one subject has only one time.\n")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	122 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	123 tres <- data.frame(t(res))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	124 rownames(tres)[1] <- nameVar
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	125 cres <- list(tres, rn, fn)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	126 return(cres)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	127 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	128
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	129 ##############################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	130 lmRepeated1FF <- function(ids, ifixfact = 0, itime, isubject, ivd, ndim, nameVar = colnames(ids)[[ivd]],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	131 dffOption, pvalCutof = 0.05) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	132 ### function to perform linear mixed model with factor Time + random factor subject
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	133 ### based on lmerTest package providing functions giving the same results as SAS proc mixed
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	134
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	135
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	136 if (!is.numeric(ids[[ivd]])) stop("Dependant variable is not numeric")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	137 if (!is.factor(ids[[itime]])) stop("Repeated factor is not a factor")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	138 if (!is.factor(ids[[isubject]])) stop("Random factor is not a factor")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	139 # Could be interesting here to add an experience plan check to give back a specific error message
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	140 # in case time points are missing for some individuals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	141
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	142 time <- ids[[itime]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	143 subject <- ids[[isubject]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	144 vd <- ids[[ivd]] ## dependant variables (quatitative)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	145
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	146 # nfp : nombre de facteurs principaux + model infos + normality test
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	147 nfp <- ndim[1]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	148 # nlt number of time levels; nct number of comparisons of the time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	149 nlt <- ndim[4]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	150 nct <- ndim[5]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	151 # number of all lmer results
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	152 nresT <- nct
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	153 ## initialization of the result vector (1 line)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	154 res <- data.frame(array(rep(NA, (nfp + 4 * nresT))))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	155 colnames(res)[1] <- "resultLM"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	156
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	157 ### if at least one subject have data for only 1 time, mixed model is not possible and variable must be skip
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	158 ### after excluding NA, table function is used to seek subjects with only 1 data
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	159 ids <- ids[!is.na(ids[[ivd]]), ]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	160 skip <- length(which(table(ids[[isubject]]) == 1))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	161
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	162 if (skip == 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	163
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	164 mfl <- lmer(vd ~ time + (1 \| subject), ids) # lmer remix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	165 rsum <- summary(mfl, ddf = dffOption)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	166 ## test Shapiro Wilks on the residus of the model
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	167 rShapiro <- shapiro.test(rsum$residuals)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	168 raov <- anova(mfl, ddf = dffOption)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	169 ## Sum of square : aov$'Sum Sq', Mean square : aov$`Mean Sq`, proba : aov$`Pr(>F)`
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	170
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	171 ## Test of all differences estimates between levels as SAS proc mixed.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	172 ## results are in diffs.lsmeans.table dataframe
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	173 ## test.effs=NULL perform all pairs comparisons including interaction effect
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	174 dlsm1 <- data.frame(difflsmeans(mfl, test.effs = NULL))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	175 ddlsm1 <- dlsm1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	176 ## save rownames and factor names
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	177 rn <- rownames(ddlsm1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	178 fn <- ddlsm1[, c(1, 2)]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	179 ## writing the results on a single line
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	180 namesFactEstim <- paste("estimate ", rownames(ddlsm1)[c(1:(nct))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	181 namesFactPval <- paste("pvalue ", rownames(ddlsm1)[c(1:(nct))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	182 namesFactprinc <- "pval_time"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	183 namesLowerCI <- paste("lowerCI ", rownames(ddlsm1)[c(1:(nct))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	184 namesUpperCI <- paste("upperCI ", rownames(ddlsm1)[c(1:(nct))], sep = "")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	185
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	186 ### lmer results on 1 vector
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	187 # pvalue of shapiro Wilks test of the residuals
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	188 res[1, ] <- rShapiro$p.value; rownames(res)[1] <- "Shapiro.pvalue.residuals"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	189 res[2, ] <- rsum$varcor$subject[1] ;rownames(res)[2] <- "Subject.Variance"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	190 res[3, ] <- rsum$devcomp$cmp[7] ; rownames(res)[3] <- "REML"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	191
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	192 ### factor time pvalue results + shapiro test
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	193 res[nfp, ] <- raov[, 6]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	194 rownames(res)[nfp] <- namesFactprinc
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	195
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	196 # pvalues of time factor levels comparisons
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	197 res[(nfp + 1):(nfp + nct), ] <- ddlsm1[c(1:nct), 9]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	198 rownames(res)[(nfp + 1):(nfp + nct)] <- namesFactPval
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	199
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	200 # Estimates of time factor levels
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	201 nresf <- nresT
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	202 res[(nfp + nresf + 1):(nfp + nresf + nct), ] <- ddlsm1[c(1:nct), 3]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	203 rownames(res)[(nfp + nresf + 1):(nfp + nresf + nct)] <- namesFactEstim
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	204
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	205 # Lower CI of the difference between levels of factors
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	206 # nresf is incremeted
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	207 nresf <- nresf + nresT
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	208 res[(nfp + nresf + 1):(nfp + nresf + nct), ] <- ddlsm1[c(1:nct), 7]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	209 rownames(res)[(nfp + nresf + 1):(nfp + nresf + nct)] <- namesLowerCI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	210 # Lower CI of the difference between levels of factors
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	211 # nresf is incremeted
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	212 nresf <- nresf + nresT
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	213 res[(nfp + nresf + 1):(nfp + nresf + nct), ] <- ddlsm1[c(1:nct), 8]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	214 rownames(res)[(nfp + nresf + 1):(nfp + nresf + nct)] <- namesUpperCI
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	215
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	216
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	217 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	218 ## one of the subject has only one time, subject can't be a random variable
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	219 ## A repeated measure could be run instead function lme of package nlme, next version
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	220 res[1, ] <- NA
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	221 cat("\n Computing impossible for feature ", colnames(ids)[4], ": at least one subject has only one time.\n")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	222 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	223 tres <- data.frame(t(res))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	224 rownames(tres)[1] <- nameVar
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	225 cres <- list(tres, rn, fn)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	226 return(cres)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	227
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	228 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	229
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	230 ##############################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	231 defColRes <- function(ids, ifixfact, itime) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	232 ## define the size of the result file depending on the numbers of levels of the fixed and time factor.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	233 ## Numbers of levels define the numbers of comparisons with pvalue and estimate of the difference.
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	234 ## The result file also contains the pvalue of the fixed factor, time factor and interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	235 ## plus Shapiro normality test. This is define by nfp
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	236 ## subscript of fixed factor=0 means no other fixed factor than "time"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	237 if (ifixfact > 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	238 nfp <- 6 # shapiro + subject variance + REML + time + fixfact + interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	239 time <- ids[[itime]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	240 fixfact <- ids[[ifixfact]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	241
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	242 cat("\n Levels fixfact: ", levels(fixfact))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	243 cat("\n Levels time: ", levels(time))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	244
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	245 # ncff number of comparisons of the fixed factor (nlff number of levels of fixed factor)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	246 nlff <- length(levels(fixfact))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	247 ncff <- (nlff * (nlff - 1)) / 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	248 # nct number of comparison of the time factor (nlt number of levels of time factor)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	249 nlt <- length(levels(time))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	250 nct <- (nlt * (nlt - 1)) / 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	251 # nci number of comparison of the interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	252 nli <- nlff * nlt
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	253 nci <- (nli * (nli - 1)) / 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	254 ndim <- c(NA, NA, NA, NA, NA, NA, NA)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	255
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	256 ndim[1] <- nfp # pvalues of fixed factor, time factor and interaction (3columns) and shapiro test pvalue
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	257 ndim[2] <- nlff # number of levels of fixed factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	258 ndim[3] <- ncff # number of comparisons (2by2) of the fixed factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	259 ndim[4] <- nlt # number of levels of time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	260 ndim[5] <- nct # number of comparisons (2by2) of the time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	261 ndim[6] <- nli # number of levels of interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	262 ndim[7] <- nci # number of comparisons (2by2) of the interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	263
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	264 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	265 else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	266 nfp <- 4 # Mandatory columns: shapiro + subject variance + REML + time
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	267 time <- ids[[itime]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	268 # nct number of comparison of the time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	269 nlt <- length(levels(time))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	270 nct <- (nlt * (nlt - 1)) / 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	271 ndim <- c(NA, NA, NA, NA, NA, NA, NA)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	272
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	273 ndim[1] <- nfp # pvalues of shapiro test + subject variance + REML + time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	274 ndim[4] <- nlt # number of levels of time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	275 ndim[5] <- nct # number of comparisons (2by2) of the time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	276 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	277 return(ndim)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	278 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	279
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	280 ##############################################################################################################
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	281 lmixedm <- function(datMN,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	282 samDF,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	283 varDF,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	284 fixfact, time, subject,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	285 logtr = "none",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	286 pvalCutof = 0.05,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	287 pvalcorMeth = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")[7],
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	288 dffOption,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	289 visu = "no",
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	290 least.confounded = FALSE,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	291 outlier.limit = 3,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	292 pdfC,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	293 pdfE
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	294 ) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	295 sampids <- samDF
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	296 dataMatrix <- datMN
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	297 varids <- varDF
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	298
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	299 options("scipen" = 50, "digits" = 5)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	300 pvalCutof <- as.numeric(pvalCutof)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	301
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	302 cat("\n dff computation method=", dffOption)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	303 ### Function running lmer function on a set of variables described in
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	304 ### 3 different dataframes as used by W4M
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	305 ### results are merge with the metadata variables varids
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	306 ### ifixfact, itime, isubject are subscripts of the dependant variables. if only time factor the ifixfat is set to 0 and no diag is performed (visu="no")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	307 if (fixfact == "none") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	308 ifixfact <- 0 ; visu <- "no"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	309 } else ifixfact <- which(colnames(sampids) == fixfact)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	310 itime <- which(colnames(sampids) == time)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	311 isubject <- which(colnames(sampids) == subject)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	312
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	313 lmmds <- dataMatrix
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	314 if (logtr != "log10" & logtr != "log2") logtr <- "none"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	315 if (logtr == "log10") lmmds <- log10(lmmds + 1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	316 if (logtr == "log2") lmmds <- log2(lmmds + 1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	317
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	318 dslm <- cbind(sampids, lmmds)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	319
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	320 nvar <- ncol(lmmds)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	321 firstvar <- ncol(sampids) + 1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	322 lastvar <- firstvar + ncol(lmmds) - 1
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	323
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	324 if (ifixfact > 0) dslm[[ifixfact]] <- factor(dslm[[ifixfact]])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	325 dslm[[itime]] <- factor(dslm[[itime]])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	326 dslm[[isubject]] <- factor(dslm[[isubject]])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	327 ## call defColres to define the numbers of test and so the number of columns of results
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	328 ## depends on whether or not there is a fixed factor with time. If only time factor ifixfact=0
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	329 if (ifixfact > 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	330 ndim <- defColRes(dslm[, c(ifixfact, itime)], ifixfact = 1, itime = 2)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	331 nColRes <- ndim[1] + (4 * (ndim[3] + ndim[5] + ndim[7]))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	332 firstpval <- ndim[1] - 2
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	333 lastpval <- ndim[1] + ndim[3] + ndim[5] + ndim[7]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	334 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	335 ndim <- defColRes(dslm[, itime], ifixfact = 0, itime = 1)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	336 nColRes <- ndim[1] + (4 * (ndim[5]))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	337 firstpval <- ndim[1]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	338 lastpval <- ndim[1] + ndim[5]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	339 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	340 ## initialisation of the result file
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	341 resLM <- data.frame(array(rep(NA, nvar * nColRes), dim = c(nvar, nColRes)))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	342 rownames(resLM) <- rownames(varids)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	343
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	344 ## PDF initialisation
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	345 if (visu == "yes") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	346 pdf(pdfC, onefile = TRUE, height = 15, width = 30)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	347 par(mfrow = c(1, 3))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	348 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	349
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	350
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	351 for (i in firstvar:lastvar) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	352
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	353 subds <- dslm[, c(ifixfact, itime, isubject, i)]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	354
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	355 tryCatch({
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	356 if (ifixfact > 0)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	357 reslmer <- lmRepeated2FF(subds, ifixfact = 1, itime = 2, isubject = 3, ivd = 4, ndim = ndim, visu = visu,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	358 tit = colnames(dslm)[i], pvalCutof = pvalCutof,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	359 dffOption = dffOption, least.confounded = least.confounded,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	360 outlier.limit = outlier.limit)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	361 else
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	362 reslmer <- lmRepeated1FF(subds, ifixfact = 0, itime = 1, isubject = 2, ivd = 3, ndim = ndim,
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	363 pvalCutof = pvalCutof, dffOption = dffOption)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	364
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	365 resLM[i - firstvar + 1, ] <- reslmer[[1]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	366 }, error = function(e) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	367 cat("\nERROR with ", rownames(resLM)[i - firstvar + 1], ": ", conditionMessage(e), "\n")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	368 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	369 )
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	370
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	371 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	372
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	373 if (exists("reslmer")) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	374 colnames(resLM) <- colnames(reslmer[[1]])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	375 labelRow <- reslmer[[2]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	376 factorRow <- reslmer[[3]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	377 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	378 stop("\n- - - - -\nModel computation impossible for every single variables in the dataset: no result returned.\n- - - - -\n")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	379 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	380
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	381 if (visu == "yes") dev.off()
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	382
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	383
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	384 ## pvalue correction with p.adjust library multtest
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	385 ## Possible methods of pvalue correction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	386 AdjustMeth <- c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	387 if (length(which(pvalcorMeth == AdjustMeth)) == 0) pvalcorMeth <- "none"
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	388
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	389 if (pvalcorMeth != "none") {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	390 for (k in firstpval:lastpval) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	391 resLM[[k]] <- p.adjust(resLM[[k]], method = pvalcorMeth, n = dim(resLM[k])[[1]])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	392
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	393 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	394 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	395
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	396 ## for each variables, set pvalues to NA and estimates = 0 when pvalue of factor > pvalCutof value define by user
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	397 if (ifixfact > 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	398 ## time effect
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	399 resLM[which(resLM[, firstpval] > pvalCutof), c((lastpval + 1):(lastpval + ndim[5]))] <- 0
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	400 resLM[which(resLM[, firstpval] > pvalCutof), c((ndim[1] + 1):(ndim[1] + ndim[5]))] <- NA
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	401 ## treatment effect
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	402 resLM[which(resLM[, firstpval + 1] > pvalCutof), c((lastpval + ndim[5] + 1):(lastpval + ndim[5] + ndim[3]))] <- 0
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	403 resLM[which(resLM[, firstpval + 1] > pvalCutof), c((ndim[1] + ndim[5] + 1):(ndim[1] + ndim[5] + ndim[3]))] <- NA
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	404 ## interaction effect
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	405 resLM[which(resLM[, firstpval + 2] > pvalCutof), c((lastpval + ndim[5] + ndim[3] + 1):(lastpval + ndim[5] + ndim[3] + ndim[7]))] <- 0
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	406 resLM[which(resLM[, firstpval + 2] > pvalCutof), c((ndim[1] + ndim[5] + ndim[3] + 1):(ndim[1] + ndim[5] + ndim[3] + ndim[7]))] <- NA
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	407 } else {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	408 ## time effect only
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	409 resLM[which(resLM[, firstpval] > pvalCutof), c((lastpval + 1):(lastpval + ndim[5]))] <- 0
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	410 resLM[which(resLM[, firstpval] > pvalCutof), c((firstpval + 1):(firstpval + ndim[5]))] <- NA
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	411 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	412
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	413 ## for each variable, estimates plots are performed if at least one factor is significant after p-value correction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	414 pdf(pdfE, onefile = TRUE, height = 15, width = 30)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	415
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	416 ## for each variable (in row)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	417 for (i in seq_len(nrow(resLM))) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	418
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	419 ## if any fixed factor + time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	420 if (ifixfact > 0)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	421
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	422 ## if any main factor after p-value correction is significant -> plot estimates and time course
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	423 if (length(which(resLM[i, c(4:6)] < pvalCutof)) > 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	424
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	425 ## Plot of time course by fixfact : data prep with factors and quantitative var to be plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	426 subv <- dslm[, colnames(dslm) == rownames(resLM)[i]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	427 subds <- data.frame(dslm[[ifixfact]], dslm[[itime]], dslm[[isubject]], subv)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	428 libvar <- c(fixfact, time, subject)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	429 colnames(subds) <- c(libvar, rownames(resLM)[i])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	430
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	431 ## Plot of estimates with error bars for all fixed factors and interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	432 rddlsm1 <- t(resLM[i, ])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	433 pval <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "pvalue"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	434 esti <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "estima"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	435 loci <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "lowerC"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	436 upci <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "UpperC"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	437 rddlsm1 <- data.frame(pval, esti, loci, upci, factorRow)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	438 colnames(rddlsm1) <- c("p.value", "Estimate", "Lower.CI", "Upper.CI", colnames(factorRow))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	439 rownames(rddlsm1) <- labelRow
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	440
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	441 ## function for plotting these 2 graphs
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	442 plot.res.Lmixed(rddlsm1, subds, title = rownames(resLM)[i], pvalCutof = pvalCutof)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	443
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	444 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	445
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	446 ## if only a time factor
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	447 if (ifixfact == 0)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	448
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	449 ## if time factor after p-value correction is significant -> plot time course
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	450 if (length(which(resLM[i, 4] < pvalCutof)) > 0) {
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	451
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	452 ## Plot of time course : data prep with factors and quantitative var to be plot
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	453 subv <- dslm[, colnames(dslm) == rownames(resLM)[i]]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	454 subds <- data.frame(dslm[[itime]], dslm[[isubject]], subv)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	455 libvar <- c(time, subject)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	456 colnames(subds) <- c(libvar, rownames(resLM)[i])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	457
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	458 ## Plot of estimates with error bars for all fixed factors and interaction
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	459 rddlsm1 <- t(resLM[i, ])
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	460 pval <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "pvalue"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	461 esti <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "estima"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	462 loci <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "lowerC"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	463 upci <- rddlsm1[substr(rownames(rddlsm1), 1, 6) == "upperC"]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	464 rddlsm1 <- data.frame(pval, esti, loci, upci, factorRow)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	465 colnames(rddlsm1) <- c("p.value", "Estimate", "Lower.CI", "Upper.CI", colnames(factorRow))
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	466 rownames(rddlsm1) <- labelRow
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	467
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	468 ## function for plotting these 2 graphs
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	469 plot.res.Lmixed(rddlsm1, subds, title = rownames(resLM)[i], pvalCutof = pvalCutof)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	470
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	471 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	472
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	473 }
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	474 dev.off()
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	475
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	476 ## return result file with pvalues and estimates (exclude confidence interval used for plotting)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	477 iCI <- which(substr(colnames(resLM), 4, 7) == "erCI")
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	478 resLM <- resLM[, - iCI]
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	479 resLM <- cbind(varids, resLM)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	480 return(resLM)
a4d89d47646f planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit 8d2ca678d973501b60479a8dc3f212eecd56eab8 workflow4metabolomics parents: diff changeset	481 }

Mercurial > repos > workflow4metabolomics > mixmodel4repeated_measures

annotate mixmodel_script.R @ 0:a4d89d47646f draft default tip