batchcorrection: Normalisation

annotate Normalisation_QCpool.r @ 0:b74d1d533dea draft default tip

planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde

author	ethevenot
date	Thu, 04 Aug 2016 11:40:35 -0400
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children

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0 b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	1 # Author: jfmartin
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	2 # Modified by : mpetera
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	3 ###############################################################################
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	4 # Correction of analytical effects inter and intra batch on intensities using quality control pooled samples (QC-pools)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	5 # according to the algorithm mentioned by Van der Kloet (J Prot Res 2009).
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	6 # Parameters : a dataframe of Ions intensities and an other of samples? metadata which must contains at least the three following columns :
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	7 # "batch" to identify the batches of analyses ; need at least 3 QC-pools for linear adjustment and 8 for lo(w)ess adjustment
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	8 # "injectionOrder" integer defining the injection order of all samples : QC-pools and analysed samples
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	9 # "sampleType" indicates if defining a sample with "sample" or a QC-pool with "pool"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	10 # NO MISSING DATA are allowed
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	11 # Version 0.91 insertion of ok_norm function to assess correction feasibility
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	12 # Version 0.92 insertion of slope test in ok_norm
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	13 # Version 0.93 name of log file define as a parameter of the correction function
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	14 # Version 0.94 Within a batch, test if all QCpools or samples values = 0. Definition of an error code in ok_norm function (see function for details)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	15 # Version 0.99 include non linear lowess correction.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	16 # Version 1.00 the corrected result matrix is return transposed in Galaxy
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	17 # Version 1.01 standard deviation=0 instead of sum of value=0 is used to assess constant data in ok_norm function. Negative values in corrected matrix are converted to 0.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	18 # Version 1.02 plotsituation create a result file with the error code of non execution of correction set by function ok_norm
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	19 # Version 1.03 fix bug in plot with "reg" option. suppression of ok_norm=4 condition if ok_norm function
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	20 # Version 2.00 Addition of loess function, correction indicator, plots ; modification of returned objects' format, some plots' displays and ok_norm ifelse format
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	21 # Version 2.01 Correction for pools negative values earlier in norm_QCpool
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	22 # Version 2.10 Script refreshing ; vocabulary adjustment ; span in parameters for lo(w)ess regression ; conditionning for third line ACP display ; order in loess display
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	23 # Version 2.11 ok1 and ok2 permutation (ok_norm) ; conditional display of regression (plotsituation) ; grouping of linked lignes + conditioning (normX) ; conditioning for CVplot
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	24 # Version 2.20 acplight function added from previous toolBox.R [# Version 1.01 "NA"-coding possibility added in acplight function]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	25 # Version 2.30 addition of suppressWarnings() for known and controlled warnings ; suppression of one useless "cat" message ; change in Rdata names ; 'batch(es)' in cat
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	26
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	27 ok_norm=function(qcp,qci,spl,spi,method) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	28 # Function used for one ion within one batch to determine whether or not batch correction is possible
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	29 # ok_norm values :
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	30 # 0 : no preliminary-condition problem
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	31 # 1 : standard deviation of QC-pools or samples = 0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	32 # 2 : insufficient number of QC-pools within a batch (n=3 for linear, n=8 for lowess or loess)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	33 # 3 : significant difference between QC-pools' and samples' means
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	34 # 4 : denominator =0 when on 1 pool per batch <> 0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	35 # 5 : (linear regression only) the slopes ratio ?QC-pools/samples? is lower than -0.2
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	36
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	37 ok=0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	38 if (method=="linear") {minQC=3} else {minQC=8}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	39 if (length(qcp)<minQC) { ok=2
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	40 } else {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	41 if (sd(qcp)==0 \| sd(spl)==0) { ok=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	42 } else {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	43 cvp= sd(qcp)/mean(qcp); cvs=sd(spl)/mean(spl)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	44 rttest=t.test(qcp,y=spl)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	45 reslsfit=lsfit(qci, qcp)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	46 reslsfitSample=lsfit(spl, spi)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	47 ordori=reslsfit$coefficients[1]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	48 penteB=reslsfit$coefficients[2]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	49 penteS=reslsfitSample$coefficients[2]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	50 # Significant difference between samples and pools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	51 if (rttest$p.value < 0.01) { ok=3
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	52 } else {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	53 # to avoid denominator =0 when on 1 pool per batch <> 0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	54 if (method=="linear" & length(which(((penteB*qci)+ordori)==0))>0 ){ ok=6
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	55 } else {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	56 # different sloop between samples and pools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	57 if (method=="linear" & penteB/penteS < -0.20) { ok=5 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	58 }}}}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	59 ok_norm=ok
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	60 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	61
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	62 plotsituation <- function (x, nbid,outfic="plot_regression.pdf", outres="PreNormSummary.txt",fact="batch",span="none") {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	63 # Check for all ions in every batch if linear or lo(w)ess correction is possible.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	64 # Use ok_norm function and create a file (PreNormSummary.txt) with the error code.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	65 # Also create a pdf file with plots of linear and lo(w)ess regression lines.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	66 # x: dataframe with ions in columns and samples in rows ; x is the result of concatenation of sample metadata file and ions file
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	67 # nbid: number of samples description columns (id and factors) with at least : "batch","injectionOrder","sampleType"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	68 # outfic: name of regression plots pdf file
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	69 # fact: factor to be used as categorical variable for plots and PCA.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	70 indfact =which(dimnames(x)[[2]]==fact)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	71 indtypsamp =which(dimnames(x)[[2]]=="sampleType")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	72 indbatch =which(dimnames(x)[[2]]=="batch")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	73 indinject =which(dimnames(x)[[2]]=="injectionOrder")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	74 lastIon=dim(x)[2]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	75 nbi=lastIon-nbid # Number of ions = total number of columns - number of identifying columns
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	76 nbb=length(levels(x$batch)) # Number of batch = number of levels of "batch" comlumn (factor)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	77 nbs=length(x$sampleType[x$sampleType=="sample"])# Number of samples = number of rows with "sample" value in sampleType
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	78 pdf(outfic,width=27,height=20)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	79 cat(nbi," ions ",nbb," batch(es) \n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	80 cv=data.frame(matrix(0,nrow=nbi,ncol=2))# initialisation de la dataset qui contiendra les CV avant et apres correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	81 pre_bilan=matrix(0,nrow=nbi,ncol=3*nbb) # dataset of ok_norm function results
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	82 for (p in 1:nbi) {# for each ion
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	83 par (mfrow=c(3,nbb),ask=F,cex=1.2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	84 labion=dimnames(x)[[2]][p+nbid]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	85 indpool=which(x$sampleType=="pool") # QCpools subscripts in x
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	86 pools1=x[indpool,p+nbid];
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	87 for (b in 1:nbb) {# for each batch...
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	88 xb=data.frame(x[(x$batch==levels(x$batch)[b]),c(indtypsamp,indinject,p+nbid)])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	89 indpb = which(xb$sampleType=="pool")# QCpools subscripts in the current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	90 indsp = which(xb$sampleType=="sample")# samples subscripts in the current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	91 indbt = which(xb$sampleType=="sample" \| xb$sampleType=="pool")# indices de tous les samples d'un batch pools+samples
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	92 normLinearTest=ok_norm(xb[indpb,3],xb[indpb,2], xb[indsp,3],xb[indsp,2],method="linear")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	93 normLoessTest=ok_norm(xb[indpb,3],xb[indpb,2], xb[indsp,3],xb[indsp,2],method="loess")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	94 normLowessTest=ok_norm(xb[indpb,3],xb[indpb,2], xb[indsp,3],xb[indsp,2],method="lowess")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	95 #cat(dimnames(x)[[2]][p+nbid]," batch ",b," loess ",normLoessTest," linear ",normLinearTest,"\n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	96 pre_bilan[ p,3*b-2]=normLinearTest
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	97 pre_bilan[ p,3*b-1]=normLoessTest
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	98 pre_bilan[ p,3*b]=normLowessTest
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	99 if(length(indpb)>1){
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	100 if(span=="none"){span1<-1 ; span2<-2*length(indpool)/nbs}else{span1<-span ; span2<-span}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	101 resloess=loess(xb[indpb,3]~xb[indpb,2],span=span1,degree=2,family="gaussian",iterations=4,surface="direct")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	102 resloessSample=loess(xb[indsp,3]~xb[indsp,2],span=2*length(indpool)/nbs,degree=2,family="gaussian",iterations=4,surface="direct")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	103 reslowess=lowess(xb[indpb,2],xb[indpb,3],f=span2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	104 reslowessSample=lowess(xb[indsp,2],xb[indsp,3])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	105 liminf=min(xb[indbt,3]);limsup=max(xb[indbt,3])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	106 plot(xb[indsp,2],xb[indsp,3],pch=16, main=paste(labion,"batch ",b),ylab="intensity",xlab="injection order",ylim=c(liminf,limsup))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	107 points(xb[indpb,2], xb[indpb,3],pch=5)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	108 points(cbind(resloess$x,resloess$fitted)[order(resloess$x),],type="l",col="orange")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	109 points(cbind(resloessSample$x,resloessSample$fitted)[order(resloessSample$x),],type="l",col="green",lty=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	110 points(reslowess,type="l",col="red"); points(reslowessSample,type="l",col="cyan",lty=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	111 abline(lsfit(xb[indpb,2],xb[indpb,3]),col="blue")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	112 abline(lsfit(xb[indsp,2],xb[indsp,3]),lty=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	113 legend("topright",c("pools","samples"),lty=c(1,2),bty="n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	114 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	115 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	116 # series de plot avant et apres correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	117 minval=min(x[p+nbid]);maxval=max(x[p+nbid])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	118 plot( x$injectionOrder, x[,p+nbid],col=x$batch,ylim=c(minval,maxval),ylab=labion,main=paste("avant correction CV pools=",round(cv[p,1],2)))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	119 suppressWarnings(plot.design( x[c(indtypsamp,indbatch,indfact,p+nbid)],main="effet sur facteurs avant"))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	120 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	121 dev.off()
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	122 pre_bilan=data.frame(pre_bilan)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	123 labion=dimnames(x)[[2]][nbid+1:nbi]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	124 for (i in 1:nbb) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	125 dimnames(pre_bilan)[[2]][3*i-2]=paste("batch",i,"linear")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	126 dimnames(pre_bilan)[[2]][3*i-1]=paste("batch",i,"loess")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	127 dimnames(pre_bilan)[[2]][3*i]=paste("batch",i,"lowess")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	128 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	129 bilan=data.frame(labion,pre_bilan)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	130 write.table(bilan,file=outres,sep="\t",row.names=F,quote=F)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	131 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	132
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	133
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	134 normlowess=function (xb,detail="no",vref=1,b,span=NULL) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	135 # Correction function applied to 1 ion in 1 batch. Use a lowess regression computed on QC-pools in order to correct samples intensity values
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	136 # xb : dataframe for 1 ion in columns and samples in rows.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	137 # vref : reference value (average of ion)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	138 # b : batch subscript
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	139 # nbid: number of samples description columns (id and factors) with at least : "batch","injectionOrder","sampleType"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	140 indpb = which(xb$sampleType=="pool") # pools subscripts of current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	141 indsp = which(xb$sampleType=="sample") # samples of current batch subscripts
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	142 indbt = which(xb$sampleType=="sample" \| xb$sampleType=="pool");# batch subscripts of all samples and QC-pools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	143 labion=dimnames(xb)[[2]][3]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	144 newval=xb[[3]] # initialisation of corrected values = intial values
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	145 ind <- 0 # initialisation of correction indicator
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	146 normTodo=ok_norm(xb[indpb,3],xb[indpb,2], xb[indsp,3],xb[indsp,2],method="lowess")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	147 #cat("batch:",b," dim xb=",dim(xb)," ok=",normTodo,"\n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	148 if (normTodo==0) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	149 if(length(span)==0){span2<-2*length(indpb)/length(indsp)}else{span2<-span}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	150 reslowess=lowess(xb[indpb,2],xb[indpb,3],f=span2) # lowess regression with QC-pools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	151 px=xb[indsp,2]; # vector of injectionOrder values only for samples
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	152 for(j in 1:length(indbt)) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	153 if (xb$sampleType[j]=="pool") {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	154 if (reslowess$y[which(indpb==j)]==0) reslowess$y[which(indpb==j)] <- 1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	155 newval[j]=(vref*xb[j,3]) / (reslowess$y[which(indpb==j)])}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	156 else { # for samples, the correction value cor correspond to the nearest QCpools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	157 cor= reslowess$y[which(abs(reslowess$x-px[which(indsp==j)])==min(abs(reslowess$x - px[which(indsp==j)])))]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	158 if (length(cor)>1) {cor=cor[1]}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	159 if (cor <= 0) {cor=vref} # no modification of initial value
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	160 newval[j]=(vref*xb[j,3]) / cor
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	161 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	162 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	163 if (detail=="reg") {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	164 liminf=min(xb[indbt,3]);limsup=max(xb[indbt,3])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	165 plot(xb[indsp,2],xb[indsp,3],pch=16,main=paste(labion,"batch ",b),ylab="intensity",xlab="injection order",ylim=c(liminf,limsup))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	166 points(xb[indpb,2], xb[indpb,3],pch=5)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	167 points(reslowess,type="l",col="red")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	168 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	169 ind <- 1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	170 } else {# if ok_norm <> 0 , we perform a correction based on batch samples average
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	171 moySample=mean(xb[indsp,3]);if (moySample==0) moySample=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	172 newval[indsp] = (vref*xb[indsp,3])/moySample
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	173 if(length(indpb)>0){
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	174 moypool=mean(xb[indpb,3]) ; if (moypool==0) moypool=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	175 newval[indpb] = (vref*xb[indpb,3])/moypool
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	176 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	177 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	178 newval <- list(norm.ion=newval,norm.ind=ind)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	179 return(newval)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	180 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	181
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	182 normlinear <-function (xb,detail="no",vref=1,b) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	183 # Correction function applied to 1 ion in 1 batch. Use a linear regression computed on QC-pools in order to correct samples intensity values
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	184 # xb : dataframe with ions in columns and samples in rows ; x is a result of concatenation of samples metadata file and ions file
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	185 # nbid : number of samples description columns (id and factors) with at least : "batch","injectionOrder","sampleType"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	186 indpb = which(xb$sampleType=="pool")# pools subscripts of current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	187 indsp = which(xb$sampleType=="sample")# samples of current batch subscripts
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	188 indbt = which(xb$sampleType=="sample" \| xb$sampleType=="pool") # QCpools and samples of current batch subscripts
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	189 labion=dimnames(xb)[[2]][3]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	190 newval=xb[[3]] # initialisation of corrected values = intial values
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	191 ind <- 0 # initialisation of correction indicator
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	192 normTodo=ok_norm(xb[indpb,3],xb[indpb,2], xb[indsp,3],xb[indsp,2],method="linear")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	193 #cat("batch:",b," ok=",normTodo,"\n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	194 if (normTodo==0) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	195 reslsfit=lsfit(xb[indpb,2],xb[indpb,3]) # linear regression for QCpools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	196 reslsfitSample=lsfit(xb[indsp,2],xb[indsp,3]) # linear regression for samples
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	197 ordori=reslsfit$coefficients[1]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	198 pente=reslsfit$coefficients[2]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	199 if (detail=="reg") {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	200 liminf=min(xb[indbt,3]);limsup=max(xb[indbt,3])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	201 plot(xb[indsp,2],xb[indsp,3],pch=16,
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	202 main=paste(labion,"batch ",b),ylab="intensity",xlab="injection order",ylim=c(liminf,limsup))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	203 points(xb[indpb,2], xb[indpb,3],pch=5)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	204 abline(reslsfit)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	205 abline(reslsfitSample,lty=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	206 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	207 # correction avec remise a l'echelle de la valeur de l'ion (valref)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	208 newval = (vrefxb[indbt,3]) / ((pente xb[indbt,2]) + ordori)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	209 ind <- 1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	210 } else {# if ok_norm<>0 , we perform a correction based on batch samples average.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	211 moySample=mean(xb[indsp,3]); if (moySample==0) moySample=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	212 newval[indsp] = (vref*xb[indsp,3])/moySample
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	213 if(length(indpb)>0){
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	214 moypool=mean(xb[indpb,3]) ; if (moypool==0) moypool=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	215 newval[indpb] = (vref*xb[indpb,3])/moypool
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	216 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	217 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	218 newval <- list(norm.ion=newval,norm.ind=ind)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	219 return(newval)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	220 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	221
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	222
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	223 normloess <- function (xb,detail="no",vref=1,b,span=NULL) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	224 # Correction function applied to 1 ion in 1 batch.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	225 # Use a loess regression computed on QC-pools in order to correct samples intensity values.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	226 # xb : dataframe for 1 ion in columns and samples in rows.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	227 # detail : level of detail in the outlog file.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	228 # vref : reference value (average of ion)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	229 # b : batch subscript
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	230 indpb = which(xb$sampleType=="pool") # pools subscripts of current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	231 indsp = which(xb$sampleType=="sample") # samples of current batch subscripts
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	232 indbt = which(xb$sampleType=="sample" \| xb$sampleType=="pool");# batch subscripts of all samples and QCpools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	233 labion=dimnames(xb)[[2]][3]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	234 newval=xb[[3]] # initialisation of corrected values = intial values
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	235 ind <- 0 # initialisation of correction indicator
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	236 normTodo=ok_norm(xb[indpb,3],xb[indpb,2], xb[indsp,3],xb[indsp,2],method="loess")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	237 #cat("batch:",b," dim xb=",dim(xb)," ok=",normTodo,"\n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	238 if (normTodo==0) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	239 if(length(span)==0){span1<-1}else{span1<-span}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	240 resloess=loess(xb[indpb,3]~xb[indpb,2],span=span1,degree=2,family="gaussian",iterations=4,surface="direct") # loess regression with QCpools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	241 cor=predict(resloess,newdata=xb[,2])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	242 cor[cor<=1] <- 1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	243 newval=(vref*xb[,3]) / cor
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	244 if(length(which(newval>3*(quantile(newval)[4])))>0){newval <- xb[,3]} # no modification of initial value
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	245 else {ind <- 1} # confirmation of correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	246 if (detail=="reg") { # plot
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	247 liminf=min(xb[indbt,3]);limsup=max(xb[indbt,3])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	248 plot(xb[indsp,2],xb[indsp,3],pch=16,main=paste(labion,"batch ",b),ylab="intensity",xlab="injection order",ylim=c(liminf,limsup))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	249 points(xb[indpb,2], xb[indpb,3],pch=5)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	250 points(cbind(resloess$x,resloess$fitted)[order(resloess$x),],type="l",col="red")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	251 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	252 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	253 if (ind==0) {# if ok_norm != 0 or if correction creates outliers, we perform a correction based on batch samples average
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	254 moySample=mean(xb[indsp,3]);if (moySample==0) moySample=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	255 newval[indsp] = (vref*xb[indsp,3])/moySample
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	256 if(length(indpb)>0){
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	257 moypool=mean(xb[indpb,3]) ; if (moypool==0) moypool=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	258 newval[indpb] = (vref*xb[indpb,3])/moypool
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	259 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	260 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	261 newval <- list(norm.ion=newval,norm.ind=ind)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	262 return(newval)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	263 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	264
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	265
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	266
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	267 norm_QCpool <- function (x, nbid, outfic, outlog, fact, metaion, detail="no", NormMoyPool=F, NormInt=F, method="linear",span="none")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	268 {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	269 # Correction applying linear or lowess correction function on all ions for every batch of a dataframe.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	270 # x : dataframe with ions in column and samples' metadata
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	271 # nbid: number of samples description columns (id and factors) with at least : "batch","injectionOrder","sampleType"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	272 # outfic: result corrected intensity file
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	273 # outlog: name of regression plots and PCA pdf file
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	274 # fact : factor to be used as categorical variable for plots and PCA.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	275 # metaion : dataframe of ions' metadata
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	276 # detail : level of detail in the outlog file. detail="no" ACP+histogram of CV before and after correction.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	277 # detail="plot" with plot for all batch before and after correction. detail="reg" with added plots with regression lines for all batches.
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	278 # NormMoyPool : not used
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	279 # NormInt : not used
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	280 # method : regression method to be used to correct : "linear" oo "lowess" oo "loess"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	281 indfact =which(dimnames(x)[[2]]==fact)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	282 indtypsamp=which(dimnames(x)[[2]]=="sampleType")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	283 indbatch =which(dimnames(x)[[2]]=="batch")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	284 indinject =which(dimnames(x)[[2]]=="injectionOrder")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	285 lastIon=dim(x)[2]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	286 valref=apply(as.matrix(x[,(nbid+1):(lastIon)]),2,mean) # reference value for each ion used to still have the same rought size of values
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	287 nbi=lastIon-nbid # number of ions
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	288 nbb=length(levels(x$batch)) # Number of batch(es) = number of levels of factor "batch" (can be =1)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	289 nbs=length(x$sampleType[x$sampleType=="sample"])# Number of samples
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	290 nbp=length(x$sampleType[x$sampleType=="pool"])# Number of QCpools
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	291 Xn=data.frame(x[,c(1:nbid)],matrix(0,nrow=nbp+nbs,ncol=nbi))# initialisation of the corrected dataframe (=initial dataframe)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	292 dimnames(Xn)=dimnames(x)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	293 cv=data.frame(matrix(0,nrow=nbi,ncol=2))# initialisation of dataframe containing CV before and after correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	294 dimnames(cv)[[2]]=c("avant","apres")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	295 if (detail!="reg" && detail!="plot" && detail!="no") {detail="no"}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	296 pdf(outlog,width=27,height=20)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	297 cat(nbi," ions ",nbb," batch(es) \n")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	298 if (detail=="plot") {par (mfrow=c(4,4),ask=F,cex=1.5)}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	299 res.ind <- matrix(NA,ncol=nbb,nrow=nbi,dimnames=list(dimnames(x)[[2]][-c(1:nbid)],paste("norm.b",1:nbb,sep="")))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	300 for (p in 1:nbi) {# for each ion
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	301 labion=dimnames(x)[[2]][p+nbid]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	302 if (detail == "reg") {par (mfrow=c(4,4),ask=F,cex=1.5)}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	303 indpool=which(x$sampleType=="pool")# QCpools subscripts in all batches
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	304 pools1=x[indpool,p+nbid]; cv[p,1]=sd(pools1)/mean(pools1)# CV before correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	305 for (b in 1:nbb) {# for every batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	306 indpb = which(x$batch==levels(x$batch)[b] & x$sampleType=="pool")# QCpools subscripts of the current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	307 indsp = which(x$batch==levels(x$batch)[b] & x$sampleType=="sample")# samples subscripts of the current batch
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	308 indbt = which(x$batch==levels(x$batch)[b] & (x$sampleType=="pool" \| x$sampleType=="sample")) # subscripts of all samples
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	309 # cat(dimnames(x)[[2]][p+nbid]," indsp:",length(indsp)," indpb=",length(indpb)," indbt=",length(indbt)," ")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	310 sub=data.frame(x[(x$batch==levels(x$batch)[b]),c(indtypsamp,indinject,p+nbid)])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	311 if (method=="linear") { res.norm = normlinear(sub,detail,valref[p],b)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	312 } else { if (method=="loess"){ res.norm <- normloess(sub,detail,valref[p],b,span)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	313 } else { if (method=="lowess"){ res.norm <- normlowess(sub,detail,valref[p],b,span)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	314 } else {stop("\n--\nNo valid 'method' argument supplied.\nMust be 'linear','loess' or 'lowess'.\n--\n")}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	315 }}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	316 Xn[indbt,p+nbid] = res.norm[[1]]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	317 res.ind[p,b] <- res.norm[[2]]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	318 # CV batch test : if after normaliszation, CV before < CV after initial values are kept
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	319 # moypoolRaw=mean(x[indpb,p+nbid]) ; if (moypoolRaw==0) moypoolRaw=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	320 # moySampleRaw=mean(x[indsp,p+nbid]); if (moySampleRaw==0) moySampleRaw=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	321 # moypool=mean(Xn[indpb,p+nbid]) ; if (moypool==0) moypool=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	322 # #moySample=mean(Xn[indsp,p+nbid]); if (moySample==0) moySample=1
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	323 # if (sd( Xn[indpb,p+nbid])/moypool>sd(x[indpb,p+nbid])/moypoolRaw) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	324 # Xn[indpb,p+nbid] = (valref[p]*x[indpb,p+nbid])/moypoolRaw
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	325 # Xn[indsp,p+nbid] = (valref[p]*x[indsp,p+nbid])/moySampleRaw
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	326 # }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	327 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	328 Xn[indpool,p+nbid][Xn[indpool,p+nbid]<0] <- 0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	329 pools2=Xn[indpool,p+nbid]; cv[p,2]=sd(pools2)/mean(pools2)# CV apres correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	330 if (detail=="reg" \|\| detail=="plot" ) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	331 # plot before and after correction
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	332 minval=min(cbind(x[p+nbid],Xn[p+nbid]));maxval=max(cbind(x[p+nbid],Xn[p+nbid]))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	333 plot( x$injectionOrder, x[,p+nbid],col=x$batch,ylab=labion,ylim=c(minval,maxval),main=paste("avant correction CV pools=",round(cv[p,1],2)))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	334 points(x$injectionOrder[indpool],x[indpool,p+nbid],col="maroon",pch=".",cex=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	335 plot(Xn$injectionOrder,Xn[,p+nbid],col=x$batch,ylab="",ylim=c(minval,maxval),main=paste("apres correction CV pools=",round(cv[p,2],2)))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	336 points(Xn$injectionOrder[indpool],Xn[indpool,p+nbid],col="maroon",pch=".",cex=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	337 suppressWarnings(plot.design( x[c(indtypsamp,indbatch,indfact,p+nbid)],main="effet sur facteurs avant"))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	338 suppressWarnings(plot.design(Xn[c(indtypsamp,indbatch,indfact,p+nbid)],main="effet sur facteurs apres"))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	339 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	340 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	341 ### Replacement of post correction negative values by 0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	342 Xnn=Xn
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	343 valNulle=0
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	344 for (i in c((nbid+1):dim(Xn)[2])) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	345 cneg=which(Xn[[i]]<0)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	346 Xnn[[i]]=replace(Xn[[i]],cneg,valNulle)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	347 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	348 Xn=Xnn
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	349 write.table(Xn,file=outfic,sep="\t",row.names=F,quote=F)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	350
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	351 if (detail=="reg" \|\| detail=="plot" \|\| detail=="no") {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	352 if (nbi > 3) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	353 par(mfrow=c(3,4),ask=F,cex=1.2) # PCA Plot before/after, normed only and ions plot
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	354 acplight(x[,c(indtypsamp,indbatch,indtypsamp,indfact,(nbid+1):lastIon)],"uv",TRUE)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	355 norm.ion <- which(colnames(Xn)%in%(rownames(res.ind)[which(rowSums(res.ind)>=1)]))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	356 acplight(Xn[,c(indtypsamp,indbatch,indtypsamp,indfact,(nbid+1):lastIon)],"uv",TRUE,norm.ion)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	357 if(length(norm.ion)>0){acplight(Xn[,c(indtypsamp,indbatch,indtypsamp,indfact,norm.ion)],"uv",TRUE)}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	358 par(mfrow=c(1,2),ask=F,cex=1.2) # Before/after boxplot
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	359 cvplot=cv[!is.na(cv[[1]])&!is.na(cv[[2]]),]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	360 if(nrow(cvplot)>0){
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	361 boxplot(cvplot[[1]],ylim=c(min(cvplot),max(cvplot)),main="CV avant")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	362 boxplot(cvplot[[2]],ylim=c(min(cvplot),max(cvplot)),main="CV apres")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	363 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	364 dev.off()
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	365 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	366 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	367 if (nbi<=3) {dev.off()}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	368 # transposed matrix is return (format of the initial matrix with ions in rows)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	369 Xr=Xn[,-c(1:nbid)]; dimnames(Xr)[[1]]=Xn[[1]]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	370 Xr=t(Xr) ; Xr <- data.frame(ions=rownames(Xr),Xr)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	371
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	372 res.norm[[1]] <- Xr ; res.norm[[2]] <- data.frame(metaion,res.ind) ; res.norm[[3]] <- x[,c(1:nbid)]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	373 names(res.norm) <- c("dataMatrix","variableMetadata","sampleMetadata")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	374 return(res.norm)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	375 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	376
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	377
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	378
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	379
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	380
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	381 acplight <- function(ids, scaling="uv", indiv=FALSE,indcol=NULL) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	382 suppressPackageStartupMessages(library(ade4))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	383 suppressPackageStartupMessages(library(pcaMethods))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	384 # fait une ACP sur ids sachant que la colonne 1 contient l'identificateur d'individu
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	385 # la colonne 2:nf contient les facteurs definissant la couleur des individus
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	386 for (i in 1:3) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	387 idss=ids[which(ids[,i+1]!="NA"),]
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	388 idss=data.frame(idss[idss[,i+1]!="",])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	389 classe=as.factor(idss[[i+1]])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	390 idsample=as.character(idss[[1]])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	391 colour=1:length(levels(classe))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	392 ions=as.matrix(idss[,5:dim(idss)[2]])
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	393 # choix du scaling : "uv","none","pareto"
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	394 object=suppressWarnings(prep(ions, scale=scaling, center=TRUE))
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	395 if(i==1){if(length(which(apply(ions,2,var)==0))>0){cat("Warning : there are",length(which(apply(ions,2,var)==0)),"constant ions.\n")}}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	396 # ALGO: nipals,svdImpute, Bayesian, svd, probalistic=F
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	397 result <- pca(object, center=F, method="svd", nPcs=2)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	398 # ADE4 : representation des ellipsoides des individus de chaque classe
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	399 s.class(result@scores, classe, cpoint = 1,xax=1,yax=2,col=colour,sub=sprintf("Scores - PCs %sx%s",1,2), possub="bottomright")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	400 #s.label(result@loadings,label = ions, cpoint = 0, clabel=0.4, xax=1,yax=2,sub="Loadings",possub="bottomright")
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	401 if(i==1){resulti <- result}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	402 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	403 if(indiv) {
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	404 colour <- rep("darkblue",length(resulti@loadings)) ; if(!is.null(indcol)) {colour[-c(indcol)] <- "red"}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	405 plot(resulti@loadings,col=colour,main="Loadings",xaxt="n",yaxt="n",pch=20)
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	406 abline(h=0,v=0)}
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	407 }
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	408
b74d1d533dea planemo upload for repository https://github.com/workflow4metabolomics/batchcorrection.git commit 241fb99a843e13195c5054cd9731e1561f039bde ethevenot parents: diff changeset	409

Mercurial > repos > ethevenot > batchcorrection

annotate Normalisation_QCpool.r @ 0:b74d1d533dea draft default tip