diff --git a/MedianVar/MedianVarPerseus.R b/MedianVar/MedianVarPerseus.R new file mode 100644 index 0000000..3573413 --- /dev/null +++ b/MedianVar/MedianVarPerseus.R @@ -0,0 +1,45 @@ +#devtools::install_github("cox-labs/PerseusR") +library(PerseusR) +args = commandArgs(trailingOnly=TRUE) +if (length(args) != 2) {stop(paste("This script is for calculating the median of normalized variance from a Perseus matrix table. +How to run: +args[1] - Perseus matrix table of proteinGroup table +args[2] - Row number of the annotation for sample groups +args[3] - Row number of the annotation of Type which shows E, N, C and T +args[4] - Row number of the first row of intensity values +EX: Rscript MedianVar.R proteinGroup_Perseus.txt 4 1 5\n" ,sep="\n"), call.=FALSE)} +cat("Running now...\n") +inFile <- args[1] +outFile <- args[2] +#inFile<-"C:/Users/animeshs/GD/tools/MedianVar/proteinGroup_Perseus.txt" +mdata <- read.perseus(inFile) +Samples<-mdata@annotRows$Samples +celltypes <- as.character(unique(Samples)) +Type<-mdata@annotRows$Experiments +Channel<-mdata@annotRows$Channels +Uniprot<-paste(mdata@annotCols$Protein.IDs) +counts<- main(mdata) +counts<-counts[complete.cases(counts), ] +#countz<-counts +colnames(counts)<-Samples +vars<-c() +a<-1 +for (cell in celltypes){ + counts2 <- counts[,grepl(cell, names(counts))] + nor_vars_c <- c() + l<-1 + for(j in seq(1, nrow(counts2))) { + nor_vars_c[l] <- var(unlist(counts2[j,]), na.rm=TRUE)/var(unlist(counts[j,]), na.rm=TRUE) + l<-l+1 + } + vars[a]<-median(nor_vars_c,na.rm = T) + a<-a+1 +} +#countz2<-counts2 +df <- data.frame(matrix(unlist(vars), nrow=length(vars), byrow=T)) +colnames(df)<-c("median of normalized variances") +#print(df) +outMdata <- matrixData(main=df,annotCols=as.data.frame(matrix(unlist(celltypes), nrow=length(vars), byrow=T))) +#outFile<-"C:/Users/animeshs/GD/tools/MedianVar/proteinGroup_Perseus.txt.out.txt" +write.perseus(outMdata,annotCols=celltypes, outFile) +cat("Done...\n") diff --git a/MedianVar/session1.sps b/MedianVar/session1.sps new file mode 100644 index 0000000..70d4e48 Binary files /dev/null and b/MedianVar/session1.sps differ diff --git a/README.md b/README.md index d10b99f..5b773b5 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ # tools + ## MedianVar.R This script is for calculating the median of normalized variance from a Perseus matrix table. @@ -8,3 +9,24 @@ args[2] - Row number of the annotation for sample groups
args[3] - Row number of the annotation of Type which shows E, N, C and T
args[4] - Row number of the first row of intensity values
EX: Rscript MedianVar.R proteinGroup_Perseus.txt 4 1 5
+ +## MedianVarPerseus.R +This script is for calculating same the above using [External:Matrix=>R](https://github.com/cox-labs/PluginInterop) [PerseusR](https://github.com/cox-labs/PerseusR) to call directly from [Perseus](https://maxquant.net/download_asset/perseus/1.6.15.0) after installing R: +``` +devtools::install_github("cox-labs/PerseusR") +``` + +Test: + +``` +File Generic-matrix-upload proteinGroup_Perseus.txt into Perseus +Invoke External:Matrix=>R and provide script&R location like following respectively: +script: MedianVarPerseus.R +R: Rscript.exe +``` +As shown in session1.sps. + +PS: on windows if "Error in utils::download.file(url, path, method = method, quiet = quiet, :cannot open URL 'https://api.github.com/repos/cox-labs/PerseusR/tarball/HEAD'" run "options(download.file.method = "wininet")" before installing: + +## aovPerseusR\proteinGroupsANOVA.r +R script callable via https://github.com/cox-labs/PerseusR as above that can reproduce the ANOVA p&q-values(using Benjamini/Hochberg) from [Multiple-sample tests in Perseus](http://coxdocs.org/doku.php?id=perseus:user:activities:MatrixProcessing:Tests:MultipleSampleTestProcessing): It also provides the mean-difference with posthoc/TukeyHSD corrected p-values for each group comparison as shown in the attached Perseus session. Need to be mindful that NAs are being imputed as 0 so better to take care of NAs in Perseus beforehand!  diff --git a/aovPerseusR/LICENSE.md b/aovPerseusR/LICENSE.md new file mode 100644 index 0000000..8d43dda --- /dev/null +++ b/aovPerseusR/LICENSE.md @@ -0,0 +1,20 @@ +Copyright (c) 2021- @animesh . + +Permission is hereby granted, free of charge, to any person obtaining +a copy of this software and associated documentation files (the +"Software"), to deal in the Software without restriction, including +without limitation the rights to use, copy, modify, merge, publish, +distribute, sublicense, and/or sell copies of the Software, and to +permit persons to whom the Software is furnished to do so, subject to +the following conditions: + +The above copyright notice and this permission notice shall be +included in all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, +EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF +MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE +LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION +OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION +WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. diff --git a/aovPerseusR/README.md b/aovPerseusR/README.md new file mode 100644 index 0000000..fcf42cb --- /dev/null +++ b/aovPerseusR/README.md @@ -0,0 +1,41 @@ +## proteinGroupsANOVA.r +R script callable via https://github.com/cox-labs/PerseusR that can reproduce the ANOVA p&q-values(using Benjamini/Hochberg) from [Multiple-sample tests in Perseus](http://coxdocs.org/doku.php?id=perseus:user:activities:MatrixProcessing:Tests:MultipleSampleTestProcessing): It also provides the mean-difference with posthoc/TukeyHSD corrected p-values for each group comparison as shown in the attached Perseus session. Need to be mindful that NAs are being imputed as 0 so better to take care of NAs in Perseus beforehand!  + +## pre-requisites +[R](https://cloud.r-project.org/), [devtools](https://www.r-project.org/nosvn/pandoc/devtools.html) and [PerseusR](https://github.com/cox-labs/PerseusR) , note on windows if +`"Error in utils::download.file(url, path, method = method, quiet = quiet, :cannot open URL 'https://api.github.com/repos/cox-labs/PerseusR/tarball/HEAD'" +`use +`options(download.file.method = "wininet")` +followed by install +`devtools::install_github("cox-labs/PerseusR")` within R session + +## usage +Download [Perseus](https://maxquant.net/download_asset/perseus/latest) and invoke [External:Matrix=>R](https://github.com/cox-labs/PluginInterop) with following parameters: +script: \proteinGroupsANOVA.r +R: \Rscript.exe + +## test +``` +aovt<-anova(lm(c(-0.267558, -1.34843, -0.736034, -0.950788, -0.631172, -1.35648, -0.338978, 0.179467, -1.38368, -0.374963, -0.0118891, 0.583722, 0.646115, 2.28853, -0.117149)~c(rep("g1",5),rep("g2",5),rep("g3",5)))) +summary.lm(aovt) +aovt<-aov(c(-0.267558, -1.34843, -0.736034, -0.950788, -0.631172, -1.35648, -0.338978, 0.179467, -1.38368, -0.374963, -0.0118891, 0.583722, 0.646115, 2.28853, -0.117149)~c(rep("g1",5),rep("g2",5),rep("g3",5))) #0.0134 +summary(aovt)[[1]][["Pr(>F)"]][[1]] +postHoc<-TukeyHSD(aovt,ordered = TRUE) +names(postHoc)<-"compare" +postHoc<-data.frame(postHoc$compare) +diff<-t(postHoc["diff"]) +plot(TukeyHSD(aovt)) +padj<-sapply(postHoc["p.adj"],as.numeric) +-log10(padj) + p.adj +[1,] 0.019911 +[2,] 1.720245 +[3,] 1.495404 +``` + +comparison to Perseus session session.sps file: +``` +Group1 Group2 Group3 C: ANOVA Significant N: ANOVA p value N: ANOVA q-value T: Name T: Significant pairs +-1.72025 -1.49541 1.72025 0.0134469 0.644 Row 12 Group3_Group1;Group3_Group2 +``` +but note that first values/-1.72025 in Perseus is -(thirdvalue)/1.72025 though Group3 could very well be -Group2 i.e. log10(g3-g2) =>  -1.4954 which is log10(0.0319592) from R. Probably it was decided to base G3 from g3-g1 and not g3-g3 because of the fact that 0.0190439 < 0.0319592 ? Unfortunately, the [Source code: not public](http://coxdocs.org/doku.php?id=perseus:user:activities:MatrixProcessing:Tests:MultipleSampleTestProcessing), hope it soon is https://github.com/cox-labs @JurgenCox diff --git a/aovPerseusR/matrix.out b/aovPerseusR/matrix.out new file mode 100644 index 0000000..a710025 --- /dev/null +++ b/aovPerseusR/matrix.out @@ -0,0 +1,103 @@ +Column.1 Column.2 Column.3 Column.4 Column.5 Column.6 Column.7 Column.8 Column.9 Column.10 Column.11 Column.12 Column.13 Column.14 Column.15 medianVal MinusLog10PValue medianFold CorrectedPValueBH ANOVApVal g2.g1 g3.g1 g3.g2 Group2.Group1.PvalueTukeyHSD Group3.Group1.PvalueTukeyHSD Group3.Group2.PvalueTukeyHSD Group2.Group1.mLog10PvalueTukeyHSD Group3.Group1.mLog10PvalueTukeyHSD Group3.Group2.mLog10PvalueTukeyHSD Name +#!{Type}E E E E E E E E E E E E E E E E E E E E E E E E E E E E E T +#!{C:Grouping}Group1 Group1 Group1 Group1 Group1 Group2 Group2 Group2 Group2 Group2 Group3 Group3 Group3 Group3 Group3 AOV AOV AOV 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1.26568365097046 -0.175107926130295 -2.14883828163147 1.19341707229614 1.8751722574234 -0.418384462594986 1.62833261489868 -1.11773347854614 -0.587157607078552 -0.0534929893910885 -0.395568132400513 -0.297157108783722 Row 100 diff --git a/aovPerseusR/parameters.xml b/aovPerseusR/parameters.xml new file mode 100644 index 0000000..81fcee4 --- /dev/null +++ b/aovPerseusR/parameters.xml @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/aovPerseusR/proteinGroupsANOVA.r b/aovPerseusR/proteinGroupsANOVA.r new file mode 100644 index 0000000..d8c044d --- /dev/null +++ b/aovPerseusR/proteinGroupsANOVA.r @@ -0,0 +1,121 @@ +#options(download.file.method = "wininet") +#install.packages("devtools") +#devtools::install_github("cox-labs/PerseusR") +library(PerseusR) +args = commandArgs(trailingOnly=TRUE) +if (length(args) != 2) {stop("NOTE: NaN imputed with 0 AND using Samples/last-categorical-annotation-row as groups, DONT supply any argument(s)!", call.=FALSE)} +inFile <- args[1] +outFile <- args[2] +#mCol <- args[3] +#inFile<-"L:/GD/tools/aovPerseusR/matrix.txt" +#outFile<-"L:/GD/tools/aovPerseusR/matrix.out" +mdata <- read.perseus(inFile) +mainMatrix <- main(mdata) +#dim(mainMatrix) +#summary(mainMatrix) +mdata@imputeData[is.na(mainMatrix)]="True" +mainMatrix[is.na(mainMatrix)]<-0 +#mainMatrix<-mainMatrix[complete.cases(mainMatrix),] +#samples<-mdata@annotRows$Grouping +samples<-t(mdata@annotRows[ncol(mdata@annotRows)]) +#aovt=aov(as.double(mainMatrix[2,])~as.character(samples)) +#dim(mainMatrix) +options(nwarnings = 1000000) +#pValANOVA=apply(mainMatrix, 1,function(x) summary(aov(as.double(x)~as.character(samples)))[[1]][["Pr(>F)"]][[1]]) +resANOVA=apply(mainMatrix, 1,function(x){ + aovt=aov(as.double(x)~as.character(samples)) + pval=summary(aovt)[[1]][["Pr(>F)"]][[1]] + postHoc<-TukeyHSD(aovt) + names(postHoc)<-"compare" + postHoc<-data.frame(postHoc$compare) + padj<-postHoc["p.adj"] + diff<-postHoc["diff"] + paste(pval,padj,diff,paste(rownames(postHoc),collapse="--GROUPS--"),sep="--VALS--") + } +) +pValANOVA<-sapply(strsplit(resANOVA, "--VALS--",fixed=T), "[", 1) +pValANOVA<-sapply(pValANOVA,as.numeric) +#hist(pValANOVA) +groupsANOVA<-sapply(strsplit(resANOVA, "--VALS--",fixed=T), "[", 4) +groupsANOVA<-strsplit(groupsANOVA, "--GROUPS--",fixed=T) +if(unique(unique(groupsANOVA)[[1]]==unique(groupsANOVA[[1]]))){ + padjv=sapply(strsplit(resANOVA, "--VALS--",fixed=T), "[", 2) + padjv=data.frame(padjv) + #eval(padjv) + padjv=data.frame(do.call("rbind", strsplit(as.character(padjv$padjv), "c|\\(|\\)|\\,"))) + padjv=padjv[,3:ncol(padjv)] + padjv=sapply(padjv, as.numeric) + #hist(padjv) + mlog10padjv=-log10(padjv) + #hist(mlog10padjv) + colnames(padjv)<-paste(groupsANOVA[[1]],"PvalueTukeyHSD",sep="-") + colnames(mlog10padjv)<-paste(groupsANOVA[[1]],"mLog10PvalueTukeyHSD",sep="-") + diffv=sapply(strsplit(resANOVA, "--VALS--",fixed=T), "[", 3) + diffv=data.frame(diffv) + diffv=data.frame(do.call("rbind", strsplit(as.character(diffv$diffv), "c|\\(|\\)|\\,"))) + diffv=diffv[,3:ncol(diffv)] + diffv=sapply(diffv, as.numeric) + #hist(diffv) + colnames(diffv)<-paste(groupsANOVA[[1]],"Difference",sep="-") + #hist(padjv$X2) + #eval(padjv$padjv[1]) + #strsplit(as.character(padjv[,1]), " ",fixed=T) + #split(padjv, " ") + #unique(sapply(strsplit(groupsANOVA, "---",fixed=T), "[", c(1))) +} +#summary(warnings()) +#tc=apply(mainMatrix, 1, function(x) tryCatch(TukeyHSD(aov(x~samples,"Sample", ordered = TRUE)),error=function(x){return(rep(1,20))})}) tryCatch(TukeyHSD(aov(x~factorC,"factorC")),error=function(x){return(rep(1,20))})}) +#outMdata <- matrixData(main=as.data.frame(pValANOVA)) +#anova(lm(as.numeric(dataNorm[2,])~factorC*factorS)) +#aov((as.numeric(dataNorm[2,])~factorC*factorS)) +#TukeyHSD(aov((as.numeric(dataNorm[2,])~factorC*factorS))) +#tc=apply(dataNorm,1,function(x){ + #tc=apply(dataNorm, 1, function(x) +# tryCatch(TukeyHSD(aov(x~factorC*factorS),"factorC:factorS", ordered = TRUE),error=function(x){return(rep(1,15))})}) +#wval=t(sapply(names(tc),function(x){tryCatch(tc[[x]]$`factorC:factorS`[46:60],error=function(x){return(rep(1,15))})})) +#write.table(wval,outF,sep="\t") +#tc$`F7A0B0;P04370-9;F6ZIA4;P04370-7` +#dataNorm[grep("F7A",row.names(data)),] +#try(TukeyHSD(aov((x~factorC*factorS))))) +#tcold$`A0A087WNP6;Q4VAA2-2;Q4VAA2;A0A087WRM0;F8WGL9;A0A087WS49` +#plot(tc$`A0A087WNP6;Q4VAA2-2;Q4VAA2;A0A087WRM0;F8WGL9;A0A087WS49`) +#write.table(t(tc),sep = "\t") +#outF = paste0(inpF,"anovaTukey.txt") +#class(tc) +#names(tc) +#do.call(rbind, lapply(names(tc), function(x) data.frame(c(ID=x, tc$x$`factorC:factorS`)))) +#lapply(names(tc), function(x) write.table(t(t(tcold[[x]]$`factorC:factorS`)[4,]),outF,sep = "\t")) +#write.table(t(sapply(tc, +# function(x){tryCatch(x$`factorC:factorS`)})),sep="\t") +#function(x){tryCatch(x$`factorC:factorS`,error=function(x){return(NULL)})})),outF,sep="\t") +#write.table(t(t(tc$x$`factorC:factorS`)[4,]),sep = "\t") +#write.table(t(t(tc$`A0A087WNP6;Q4VAA2-2;Q4VAA2;A0A087WRM0;F8WGL9;A0A087WS49`$`factorC:factorS`)[4,]),sep = "\t") +#dump(tc, file=outF) +#log10(.Machine$double.xmin) +pValNAminusdif10 = -log10(pValANOVA+.Machine$double.xmin) +#hist(pValNAminusdif10) +pValBHna = p.adjust(pValANOVA,method = "BH") +#hist(pValBHna) +pValBHnaMinusdif10 = -log10(pValBHna+.Machine$double.xmin) +#hist(pValBHnaMinusdif10) +logFCmedianGrp = apply( + mainMatrix, 1, function(x) + median(x[c(1:ncol(mainMatrix))],na.rm=T) ) +#hist(logFCmedianGrp) + +logFCmedianGrp[is.nan(logFCmedianGrp)]=0 + +logFCmedian = logFCmedianGrp#-logFCmedianGrp +logFCmedianFC = 2^(logFCmedian+.Machine$double.xmin) +#hist(logFCmedianFC) +log2FCmedianFC=log2(logFCmedianFC) +#hist(log2FCmedianFC) +aov.results = data.frame(mainMatrix,medianVal=logFCmedian,MinusLog10PValue=pValNAminusdif10,medianFold=logFCmedianFC,CorrectedPValueBH=pValBHna,ANOVApVal=pValANOVA,diffv,padjv,mlog10padjv)#,resANOVA) +#dim(aov.results) +#dim(mainMatrix) +dfANOVA=data.frame(matrix("AOV", nrow = (ncol(aov.results)-ncol(mainMatrix)), ncol = ncol(mdata@annotRows))) +colnames(dfANOVA)=colnames(mdata@annotRows) +dfANOVA=rbind(mdata@annotRows,dfANOVA) +#dim(dfANOVA) +#df[nrow(df) + 1,] = rep("ANOVA",ncol(df)) +write.perseus(aov.results, outFile,imputeData=mdata@imputeData,qualityData = mdata@qualityData,annotCols=mdata@annotCols,annotRows=dfANOVA) diff --git a/aovPerseusR/session.sps b/aovPerseusR/session.sps new file mode 100644 index 0000000..146ac53 Binary files /dev/null and b/aovPerseusR/session.sps differ