mixmodel4repeated_measures: mixmodel

annotate mixmodel_script.R @ 0:1422de181204 draft

planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50

author	jfrancoismartin
date	Wed, 10 Oct 2018 05:18:42 -0400
parents
children

rev	line source
0 1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	1 ####### R functions to perform linear mixed model for repeated measures
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	2 ####### on a multi var dataset using 3 files as used in W4M
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	3 ##############################################################################################################
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	4 lmRepeated2FF <- function(ids, ifixfact, itime, isubject, ivd, ndim, nameVar=colnames(ids)[[ivd]],
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	5 pvalCutof=0.05,dffOption, visu , tit = "", least.confounded = FALSE, outlier.limit =3)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	6 {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	7 ### function to perform linear mixed model with 1 Fixed factor + Time + random factor subject
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	8 ### based on lmerTest package providing functions giving the same results as SAS proc mixed
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	9 options(scipen = 50, digits = 5)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	10
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	11 if (!is.numeric(ids[[ivd]])) {stop("Dependant variable is not numeric")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	12 if (!is.factor(ids[[ifixfact]])) {stop("fixed factor is not a factor")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	13 if (!is.factor(ids[[itime]])) {stop("Repeated factor is not a factor")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	14 if (!is.factor(ids[[isubject]])) {stop("Random factor is not a factor")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	15 # a ce stade, il faudrait pr?voir des tests sur la validit? du plan d'exp?rience
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	16
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	17 time <- ids[[itime]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	18 fixfact <- ids[[ifixfact]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	19 subject <- ids[[isubject]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	20 vd <- ids[[ivd]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	21
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	22 # argument of the function instead of re re-running ndim <- defColRes(ids,ifixfact,itime)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	23 # nfp : number of main factors + model infos (REML, varSubject) + normality test
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	24 nfp <- ndim[1];
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	25 # ncff number of comparison of the fixed factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	26 nlff <- ndim[2]; ncff <- ndim[3]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	27 # nct number of comparison of the time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	28 nlt <- ndim[4] ; nct <- ndim[5]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	29 # nci number of comparison of the interaction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	30 nli <- ndim[6]; nci <- ndim[7]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	31 # number of all lmer results
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	32 nresT <- ncff+nct+nci
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	33 ## initialization of the result vector (1 line)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	34 ## 4 * because nresf for : pvalues + Etimates + lower CI + Upper CI
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	35 res <- data.frame(array(rep(NA,(nfp + 4 * nresT))))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	36 colnames(res)[1] <- "resultLM"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	37
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin 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
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	39 ### after excluding NA, table function is used to seek subjects with only 1 data
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	40 ids <- ids[!is.na(ids[[ivd]]),]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	41 skip <- length(which(table(ids[[isubject]])==1))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	42
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	43 if (skip==0) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	44
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	45 mfl <- lmer( vd ~ time + fixfact + time:fixfact + (1\| subject), ids) # lmer remix
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	46
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	47 # ## NL add
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	48 # ### DEPLACE APRES CALCUL PVALUES AJUSTEES ET NE FAIRE QUE SI AU MOINS 1 FACTEUR SIGNIFICATIF
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	49 # if(visu) diagmflF(mfl, title = tit, least.confounded = least.confounded, outlier.limit = outlier.limit)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	50 # ## end of NL add
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	51
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	52 rsum <- summary(mfl,ddf = dffOption)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	53 ## test Shapiro Wilks on the residus of the model
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	54 rShapiro <- shapiro.test(rsum$residuals)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	55 raov <- anova(mfl,ddf = dffOption)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	56 dlsm1 <- data.frame(difflsmeans(mfl,test.effs=NULL))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	57 ddlsm1 <- dlsm1
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	58 ## save rownames and factor names
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	59 rn <- rownames(ddlsm1)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	60 fn <- ddlsm1[,c(1,2)]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	61 ## writing the results on a single line
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	62 namesFactEstim <- paste("estimate ",rownames(ddlsm1)[c(1:(nct+ncff))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	63 namesFactPval <- paste("pvalue ",rownames(ddlsm1)[c(1:(nct+ncff))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	64 namesInter <- rownames(ddlsm1)[-c(1:(nct+ncff))]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	65 #ncI <- nchar(namesInter)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	66 namesEstimate <- paste("estimate ",namesInter)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	67 namespvalues <- paste("pvalue ",namesInter)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	68 namesFactprinc <- c("pval_time","pval_trt","pval_inter")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	69 namesFactEstim <- paste("estimate ",rownames(ddlsm1)[c(1:(nct+ncff))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	70
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	71 namesFactLowerCI <- paste("lowerCI ",rownames(ddlsm1)[c(1:(nct+ncff))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	72 namesLowerCI <- paste("lowerCI ",namesInter,sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	73
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	74 namesFactUpperCI <- paste("UpperCI ",rownames(ddlsm1)[c(1:(nct+ncff))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	75 namesUpperCI <- paste("UpperCI ",namesInter,sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	76
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	77
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	78 ### lmer results on 1 vector row
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	79 # pvalue of shapiro Wilks test of the residuals
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	80 res[1,] <- rShapiro$p.value; rownames(res)[1] <- "Shapiro.pvalue.residuals"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	81 res[2,] <- rsum$varcor$subject[1] ;rownames(res)[2] <- "Subject.Variance"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	82 res[3,] <- rsum$devcomp$cmp[7] ; rownames(res)[3] <- "REML"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	83 ### 3 principal factors pvalues results + shapiro test => nfp <- 4
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	84 res[c((nfp-2):nfp),] <- raov[,6]; rownames(res)[c((nfp-2):nfp)] <- namesFactprinc
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	85
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	86 #################### Residuals diagnostics for significants variables #########################
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	87 ### Il at least 1 factor is significant and visu=TRUE NL graphics add to pdf
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	88 ## ajout JF du passage de la valeur de p-value cutoff
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	89 if (length(which(raov[,6]<=pvalCutof))>0 & visu == 'yes') {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	90 diagmflF(mfl, title = tit, pvalCutof = pvalCutof, least.confounded = least.confounded,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	91 outlier.limit = outlier.limit)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	92
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	93 cat(" Signif ",pvalCutof)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	94
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	95
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	96 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	97
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	98 # pvalue of fixed factor comparisons
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	99 nresf <- nresT
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	100 res[(nfp+1):(nfp+nct),] <- ddlsm1[c(1:nct),9]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	101 res[(nfp+nct+1):(nfp+nct+ncff),] <- ddlsm1[(nct+1):(nct+ncff),9]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	102 rownames(res)[(nfp+1):(nfp+nct+ncff)] <- namesFactPval
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	103 res[(nfp+nct+ncff+1):(nfp+nresf),] <- ddlsm1[(nct+ncff+1):(nresT),9]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	104 rownames(res)[(nfp+nct+ncff+1):(nfp+nresT)] <- namespvalues
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	105 # Estimate of the difference between levels of factors
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	106 res[(nfp+nresf+1):(nfp+nresf+nct),] <- ddlsm1[c(1:nct),3]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	107 res[(nfp+nresf+nct+1):(nfp+nresf+nct+ncff),] <- ddlsm1[(nct+1):(nct+ncff),3]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	108 rownames(res)[(nfp+nresf+1):(nfp+nresf+nct+ncff)] <- namesFactEstim
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	109 res[(nfp+nresf+nct+ncff+1):(nfp+2*nresf),] <- ddlsm1[(nct+ncff+1):(nresT),3]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	110 rownames(res)[(nfp+nresf+nct+ncff+1):(nfp+2*nresf)] <- namesEstimate
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	111 # lower CI of the difference between levels of factors
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	112 nresf <- nresf + nresT
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	113 res[(nfp+nresf+1):(nfp+nresf+nct),] <- ddlsm1[c(1:nct),7]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	114 res[(nfp+nresf+nct+1):(nfp+nresf+nct+ncff),] <- ddlsm1[(nct+1):(nct+ncff),7]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	115 rownames(res)[(nfp+nresf+1):(nfp+nresf+nct+ncff)] <- namesFactLowerCI
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	116 res[(nfp+nresf+nct+ncff+1):(nfp+2*nresf),] <- ddlsm1[(nct+ncff+1):(nresf),7]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	117 rownames(res)[(nfp+nresf+nct+ncff+1):(nfp+nresf+(nresf/2))] <- namesLowerCI
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	118 # Upper CI of the difference between levels of factors
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	119 nresf <- nresf + nresT
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	120 res[(nfp+nresf+1):(nfp+nresf+nct),] <- ddlsm1[c(1:nct),8]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	121 res[(nfp+nresf+nct+1):(nfp+nresf+nct+ncff),] <- ddlsm1[(nct+1):(nct+ncff),8]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	122 rownames(res)[(nfp+nresf+1):(nfp+nresf+nct+ncff)] <- namesFactUpperCI
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	123 res[(nfp+nresf+nct+ncff+1):(nfp+nresf+(nresT)),] <- ddlsm1[(nct+ncff+1):(nresT),8]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	124 rownames(res)[(nfp+nresf+nct+ncff+1):(nfp+nresf+(nresT))] <- namesUpperCI
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	125
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	126
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	127 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	128 else
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	129 ## one of the subject has only one time, subject can't be a random variable
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	130 ## A repeated measure could be run instead function lme of package nlme, next version
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	131 { res[1,] <- NA
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	132 #cat("impossible computing\n")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	133
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	134 # # ## NL add (useless)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	135 # if(visu){
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	136 # grid.arrange(ggplot(data.frame()) + geom_point() + xlim(-1, 1) + ylim(-1, 1)+
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	137 # annotate("text", x = 0, y = 0, label = "impossible computing")+
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	138 # xlab(NULL) + theme(axis.text.x=element_blank(),axis.ticks.x=element_blank())+
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	139 # ylab(NULL) + theme(axis.text.y=element_blank(),axis.ticks.y=element_blank())+
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	140 # theme(panel.grid.minor = element_blank() ,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	141 # panel.grid.major = element_blank() ,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	142 # panel.background = element_rect(fill = "white"))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	143 # , top = textGrob(tit,gp=gpar(fontsize=40,font=4)))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	144 #
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	145 # }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	146 # # ## end of NL add
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	147
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	148 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	149 tres <- data.frame(t(res)); rownames(tres)[1] <- nameVar
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	150 cres <- list(tres,rn, fn)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	151 return(cres)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	152 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	153
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	154 ##############################################################################################################
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	155 lmRepeated1FF <- function(ids, ifixfact=0, itime, isubject, ivd, ndim, nameVar=colnames(ids)[[ivd]],
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	156 dffOption,pvalCutof=0.05)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	157 {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	158 ### function to perform linear mixed model with factor Time + random factor subject
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	159 ### based on lmerTest package providing functions giving the same results as SAS proc mixed
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	160
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	161 if (!is.numeric(ids[[ivd]])) {stop("Dependant variable is not numeric")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	162 if (!is.factor(ids[[itime]])) {stop("Repeated factor is not a factor")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	163 if (!is.factor(ids[[isubject]])) {stop("Random factor is not a factor")}
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	164 # a ce stade, il faudrait pr?voir des tests sur la validit? du plan d'exp?rience
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	165
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	166 time <- ids[[itime]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	167 subject <- ids[[isubject]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	168 vd <- ids[[ivd]] ## dependant variables (quatitative)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	169
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	170 # ndim <- defColRes(ids,0,itime)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	171 # nfp : nombre de facteurs principaux + model infos + normality test
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	172 nfp <- ndim[1]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	173 # nct number of comparison of the time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	174 nlt <- ndim[4] ; nct <- ndim[5]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	175 # number of all lmer results
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	176 nresf <- nct
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	177 ## initialization of the result vector (1 line)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	178 res <- data.frame(array(rep(NA,(nfp+2*nresf))))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	179 colnames(res)[1] <- "resultLM"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	180
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	181 ### if at least one subject have data for only 1 time, mixed model is not possible and variable must be skip
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	182 ### after excluding NA, table function is used to seek subjects with only 1 data
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	183 ids <- ids[!is.na(ids[[ivd]]),]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	184 skip <- length(which(table(ids[[isubject]])==1))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	185
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	186 if (skip==0) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	187
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	188 mfl <- lmer( vd ~ time + (1\| subject), ids) # lmer remix
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	189 rsum <- summary(mfl,ddf = dffOption)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	190 ## test Shapiro Wilks on the residus of the model
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	191 rShapiro <- shapiro.test(rsum$residuals)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	192 raov <- anova(mfl,ddf = dffOption)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	193 ## Sum of square : aov$'Sum Sq', Mean square : aov$`Mean Sq`, proba : aov$`Pr(>F)`
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	194
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	195 ## Test of all differences estimates between levels as SAS proc mixed.
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	196 ## results are in diffs.lsmeans.table dataframe
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	197 ## test.effs=NULL perform all pairs comparisons including interaction effect
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	198 dlsm1 <- difflsmeans(mfl,test.effs=NULL)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	199 ddlsm1 <- dlsm1$diffs.lsmeans.table
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	200
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	201 ## writing the results on a single line
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	202 namesFactEstim <- paste("estimate ",rownames(ddlsm1)[c(1:(nct))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	203 namesFactPval <- paste("pvalue ",rownames(ddlsm1)[c(1:(nct))],sep="")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	204 namesFactprinc <- "pval_time"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	205
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	206 ### lmer results on 1 vector
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	207 # pvalue of shapiro Wilks test of the residuals
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	208 res[1,] <- rShapiro$p.value; rownames(res)[1] <- "Shapiro.pvalue.residuals"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	209 res[2,] <- rsum$varcor$subject[1] ;rownames(res)[2] <- "Subject.Variance"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	210 res[3,] <- rsum$devcomp$cmp[7] ; rownames(res)[3] <- "REML"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	211
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	212 ### principal factor time pvalue results + shapiro test
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	213 res[nfp,] <- raov[,6]; rownames(res)[nfp] <- namesFactprinc
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	214 # pvalue of fixed factor comparisons
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	215 res[(nfp+1):(nfp+nct),] <- ddlsm1[c(1:nct),7]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	216 rownames(res)[(nfp+1):(nfp+nct)] <- namesFactPval
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	217
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	218 # Estimate of the difference between levels of factors
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	219 res[(nfp+nresf+1):(nfp+nresf+nct),] <- ddlsm1[c(1:nct),1]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	220 rownames(res)[(nfp+nresf+1):(nfp+nresf+nct)] <- namesFactEstim
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	221 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	222 else
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	223 ## one of the subject has only one time, subject can't be a random variable
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	224 ## A repeated measure could be run instead function lme of package nlme, next version
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	225 { res[1,] <- NA
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	226 #cat("traitement impossible\n")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	227 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	228 tres <- data.frame(t(res)); rownames(tres)[1] <- nameVar
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	229 return(tres)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	230 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	231
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	232 ##############################################################################################################
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	233 defColRes <- function(ids, ifixfact, itime) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	234 ## define the size of the result file depending on the numbers of levels of the fixed and time factor.
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	235 ## Numbers of levels define the numbers of comparisons with pvalue and estimate of the difference.
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	236 ## The result file also contains the pvalue of the fixed factor, time factor and interaction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	237 ## plus Shapiro normality test. This is define by nfp
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	238 ## subscript of fixed factor=0 means no other fixed factor than "time"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	239 if (ifixfact>0){
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	240 nfp <- 6 # shapiro+time+fixfact+interaction+ others....
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	241 time <- ids[[itime]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	242 fixfact <- ids[[ifixfact]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	243
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	244 cat("\n levels fixfact",levels(fixfact))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	245 cat("\n levels time",levels(time))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	246
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	247 # ncff number of comparisons of the fixed factor (nlff number of levels of fixed factor)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	248 nlff <- length(levels(fixfact)); ncff <- (nlff*(nlff-1))/2
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	249 # nct number of comparison of the time factor (nlt number of levels of time factor)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	250 nlt <- length(levels(time)); nct <- (nlt*(nlt-1))/2
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	251 # nci number of comparison of the interaction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	252 nli <- nlffnlt; nci <- (nli(nli-1))/2
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	253 ndim <- c(NA,NA,NA,NA,NA,NA,NA)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	254
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	255 ndim[1] <- nfp # pvalues of fixed factor, time factor and interaction (3columns) and shapiro test pvalue
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	256 ndim[2] <- nlff # number of levels of fixed factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	257 ndim[3] <- ncff # number of comparisons (2by2) of the fixed factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	258 ndim[4] <- nlt # number of levels of time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	259 ndim[5] <- nct # number of comparisons (2by2) of the time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	260 ndim[6] <- nli # number of levels of interaction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	261 ndim[7] <- nci # number of comparisons (2by2) of the interaction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	262
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	263 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	264 else {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	265 nfp <- 4 # shapiro+time
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	266 time <- ids[[itime]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	267 # nct number of comparison of the time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	268 nlt <- length(levels(time)); nct <- (nlt*(nlt-1))/2
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	269 ndim <- c(NA,NA,NA,NA,NA,NA,NA)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	270
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	271 ndim[1] <- nfp # pvalues of time factor and shapiro test pvalue
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	272 ndim[4] <- nlt # number of levels of time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	273 ndim[5] <- nct # number of comparisons (2by2) of the time factor
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	274 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	275 return(ndim)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	276 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	277
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	278 ##############################################################################################################
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	279 lmixedm <- function(datMN,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	280 samDF,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	281 varDF,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	282 fixfact, time, subject,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	283 logtr = "none",
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	284 pvalCutof = 0.05,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	285 pvalcorMeth = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")[7],
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	286 dffOption,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	287 visu = "no",
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	288 least.confounded = FALSE,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	289 outlier.limit = 3,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	290 pdfC,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	291 pdfE
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	292 )
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	293 {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	294 sampids <- samDF
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	295 dataMatrix <- datMN
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	296 varids <- varDF
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	297
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	298 options("scipen" = 50, "digits" = 5)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	299 pvalCutof <- as.numeric(pvalCutof)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	300
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	301 cat("\n dff computation method=",dffOption)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	302 ### Function running lmer function on a set of variables described in
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	303 ### 3 different dataframes as used by W4M
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	304 ### results are merge with the metadata variables varids
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	305 ### ifixfact, itime, isubject are subscripts of the dependant variables
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	306 if (fixfact=="none") ifixfact <-0 else ifixfact <- which(colnames(sampids)==fixfact)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	307 itime <- which(colnames(sampids)==time)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	308 isubject <- which(colnames(sampids)==subject)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	309
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	310 #lmmds <- dataMatrix[,-1]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	311
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	312 lmmds <- dataMatrix
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	313 if (logtr!="log10" & logtr!="log2") logtr <- "none"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	314 if (logtr=="log10") lmmds <- log10(lmmds+1)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	315 if (logtr== "log2") lmmds <- log2(lmmds+1)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	316
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	317 #idsamp <- dataMatrix[,1]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	318 #lmmds <- t(lmmds)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	319 dslm <- cbind(sampids,lmmds)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	320
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	321 nvar <- ncol(lmmds); firstvar <- ncol(sampids)+1; lastvar <- firstvar+ncol(lmmds)-1
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	322
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	323 dslm[[ifixfact]] <- factor(dslm[[ifixfact]])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	324 dslm[[itime]] <- factor(dslm[[itime]])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	325 dslm[[isubject]] <- factor(dslm[[isubject]])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	326 ## call defColres to define the numbers of test and so the number of columns of results
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	327 ## depends on whether or not there is a fixed factor with time. If only time factor ifixfact=0
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	328 if (ifixfact>0) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	329 ndim <- defColRes(dslm[,c(ifixfact,itime)],ifixfact=1,itime=2)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	330 nColRes <- ndim[1]+(4*(ndim[3]+ndim[5]+ndim[7]))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	331 firstpval <- ndim[1]-2
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	332 lastpval <- ndim[1]+ndim[3]+ndim[5]+ndim[7]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	333 } else
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	334 {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	335 ndim <- defColRes(dslm[,itime],ifixfact=0,itime=1)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	336 nColRes <- ndim[1]+(2*(ndim[5]))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	337 firstpval <- ndim[1]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	338 lastpval <- ndim[1]+ndim[5]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	339 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	340 ## initialisation of the result file
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	341 resLM <- data.frame(array(rep(NA,nvar*nColRes),dim=c(nvar,nColRes)))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	342 rownames(resLM) <- rownames(varids)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	343
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	344 ############### test ecriture dans pdf
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	345 if(visu == "yes") {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	346 pdf(pdfC, onefile=TRUE, height = 15, width = 30)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	347 par(mfrow=c(1,3))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	348 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	349 ############### fin test ecriture dans pdf
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	350 ## pour test : lastvar <- 15
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	351 cat("\n pvalCutof ", pvalCutof)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	352
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	353 for (i in firstvar:lastvar) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	354
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	355 ## NL modif
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	356 cat("\n[",colnames(dslm)[i],"] ")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	357 ## end of NL modif
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	358
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	359 subds <- dslm[,c(ifixfact,itime,isubject,i)]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	360
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	361 ## NL modif
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	362 tryCatch({
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	363 if (ifixfact>0)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	364 reslmer <- lmRepeated2FF(subds,ifixfact=1,itime=2,isubject=3, ivd=4, ndim=ndim, visu = visu,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	365 tit = colnames(dslm)[i], pvalCutof=pvalCutof,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	366 dffOption=dffOption,least.confounded = least.confounded,
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	367 outlier.limit = outlier.limit)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	368 else
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	369 reslmer <- lmRepeated1FF(subds,ifixfact=0,1,2, ivd=3, ndim=ndim, pvalCutof=pvalCutof,dffOption)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	370 ## end of NL modif
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	371 resLM[i-firstvar+1,] <- reslmer[[1]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	372 }, error=function(e){cat("ERROR : ",conditionMessage(e), "\n");})
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	373 if (i==firstvar) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	374 colnames(resLM) <- colnames(reslmer[[1]])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	375 labelRow <- reslmer[[2]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	376 factorRow <- reslmer[[3]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	377 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	378 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	379 ## for debug : ifixfact=1;itime=2;isubject=3; ivd=4;tit = colnames(dslm)[i]; ids <- subds
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	380
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	381
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	382 ## NL add
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	383 if(visu == "yes") dev.off()
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	384 ## end of NL add
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	385
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	386 ## pvalue correction with p.adjust library multtest
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	387 ## Possible methods of pvalue correction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	388 AdjustMeth <- c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY","fdr","none")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	389 if (length(which(pvalcorMeth == AdjustMeth))==0) pvalcorMeth <- "none"
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	390
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	391 if (pvalcorMeth !="none") {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	392 for (k in firstpval:lastpval){
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	393 resLM[[k]]=p.adjust(resLM[[k]], method=pvalcorMeth, n=dim(resLM[k])[[1]])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	394
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	395 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	396 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	397
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	398 ## for each variables, set pvalues to NA and estimates = 0 when pvalue of factor > pvalCutof value define by user
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	399 if (ifixfact>0) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	400 ## time effect
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	401 resLM[which(resLM[,firstpval]> pvalCutof),c((lastpval+1):(lastpval+ndim[5]))] <- 0
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	402 resLM[which(resLM[,firstpval]> pvalCutof),c((ndim[1]+1):(ndim[1]+ndim[5]))] <- NA
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	403 ## treatment effect
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	404 resLM[which(resLM[,firstpval+1]> pvalCutof),c((lastpval+ndim[5]+1):(lastpval+ndim[5]+ndim[3]))] <- 0
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	405 resLM[which(resLM[,firstpval+1]> pvalCutof),c((ndim[1]+ndim[5]+1):(ndim[1]+ndim[5]+ndim[3]))] <- NA
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	406 ## interaction effect
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	407 resLM[which(resLM[,firstpval+2]> pvalCutof),c((lastpval+ndim[5]+ndim[3]+1):(lastpval+ndim[5]+ndim[3]+ndim[7]))] <- 0
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	408 resLM[which(resLM[,firstpval+2]> pvalCutof),c((ndim[1]+ndim[5]+ndim[3]+1):(ndim[1]+ndim[5]+ndim[3]+ndim[7]))] <- NA
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	409 } else {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	410 ## time effect only
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	411 resLM[which(resLM[,firstpval]> pvalCutof),c((lastpval+1):(lastpval+ndim[5]))] <- 0
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	412 resLM[which(resLM[,firstpval]> pvalCutof),c((firstpval+1):(firstpval+ndim[5]))] <- NA
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	413 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	414
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	415 ## for each variable, estimates plots are performed if at least one factor is significant after p-value correction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	416 pdf(pdfE, onefile=TRUE, height = 15, width = 30)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	417 #par(mfrow=c(2,2))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	418
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	419 ## for each variable (in row)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	420 for (i in 1:nrow(resLM)) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	421 #cat("\n",rownames(resLM)[i])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	422 ## if any main factor after p-value correction is significant -> plot estimates and time course
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	423 if (length(which(resLM[i,c(4:6)]<pvalCutof))>0) {
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	424
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	425 ## Plot of time course by fixfact : data prep with factors and quantitative var to be plot
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	426 subv <- dslm[,colnames(dslm)==rownames(resLM)[i]]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	427 subds <- data.frame(dslm[[ifixfact]],dslm[[itime]], dslm[[isubject]],subv)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	428 #colnames(subds) <- c(colnames(dslm)[ifixfact],colnames(dslm)[itime],colnames(dslm)[isubject],rownames(resLM)[i] <- rownames(resLM)[i] )
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	429 libvar <- c(fixfact,time,subject)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	430 colnames(subds) <- c(libvar,rownames(resLM)[i])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	431
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	432 ## Plot of estimates with error bars for all fixed factors and interaction
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	433 rddlsm1 <- t(resLM[i,])
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	434 pval <- rddlsm1[substr(rownames(rddlsm1),1,6)=="pvalue"]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	435 esti <- rddlsm1[substr(rownames(rddlsm1),1,6)=="estima"]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	436 loci <- rddlsm1[substr(rownames(rddlsm1),1,6)=="lowerC"]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	437 upci <- rddlsm1[substr(rownames(rddlsm1),1,6)=="UpperC"]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	438 rddlsm1 <- data.frame(pval,esti,loci,upci,factorRow)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	439 colnames(rddlsm1) <- c("p.value","Estimate","Lower.CI","Upper.CI",colnames(factorRow))
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	440 rownames(rddlsm1) <- labelRow
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	441
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	442 ## function for plotting these 2 graphs
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	443 plot.res.Lmixed(rddlsm1, subds, title = rownames(resLM)[i], pvalCutof = pvalCutof)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	444
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	445 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	446 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	447 dev.off()
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	448
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	449 ## return result file with pvalues and estimates (exclude confidence interval used for plotting)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	450 iCI <- which(substr(colnames(resLM),4,7)=="erCI")
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	451 resLM <- resLM[,-iCI]
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	452 resLM <- cbind(varids,resLM)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	453 return(resLM)
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	454 }
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	455
1422de181204 planemo upload for repository https://github.com/workflow4metabolomics/mixmodel4repeated_measures commit 6ea32b3182383c19e5333201d2385a61d8da3d50 jfrancoismartin parents: diff changeset	456

Mercurial > repos > jfrancoismartin > mixmodel4repeated_measures

annotate mixmodel_script.R @ 0:1422de181204 draft