## ----styleSweave, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex(use.unsrturl=FALSE) ## ----include=FALSE--------------------------------------------------------- library(knitr) opts_chunk$set( concordance=TRUE ) ## ----options, echo=FALSE--------------------------------------------------- options(prompt = " ", continue = " ") ## ----CranPck, eval=TRUE, echo=TRUE----------------------------------------- Cran.pck<-c("scales", "reshape2", "plyr", "ggplot2", "ggrepel", "ggalluvial", "FactoMineR", "factoextra", "plot3D", "plot3Drgl", "UpSetR", "gprofiler2") ## ----installCranPck, eval=FALSE, echo=TRUE--------------------------------- # Select.package.CRAN<-"FactoMineR" # # # if(!require(package=Select.package.CRAN, # quietly=TRUE, character.only=TRUE, warn.conflicts=FALSE)){ # install.packages(pkgs=Select.package.CRAN, dependencies=TRUE) # }# if(!require(package=Cran.pck[i], quietly=TRUE, character.only=TRUE)) ## ----BioconductorPck, eval=TRUE, echo=TRUE--------------------------------- Bioconductor.pck<-c("Mfuzz","SummarizedExperiment","DESeq2","ComplexHeatmap") ## ----BiocManagerPck, eval=FALSE, echo=TRUE--------------------------------- # if(!require(package="BiocManager", # quietly=TRUE, character.only=TRUE, warn.conflicts=FALSE)){ # install.packages("BiocManager") # }# if(!require(package="BiocManager", quietly=TRUE, character.only=TRUE)) ## ----BiocconductorVersion, eval=FALSE, echo=TRUE--------------------------- # BiocManager::install(version = "3.16") ## ----installBioconductorpck, eval=FALSE, echo=TRUE------------------------- # Select.package.CRAN<-"DESeq2" # if(!require(package=Select.package.CRAN, # quietly=TRUE, character.only=TRUE, warn.conflicts=FALSE)){ # BiocManager::install(pkgs=Select.package.CRAN) # }# if(!require(package=Select.package.CRAN, quietly=TRUE, character.only=TRUE)) ## ----library, eval=TRUE, echo=TRUE----------------------------------------- library(MultiRNAflow) ## ----LoadMus1, echo=TRUE, eval=TRUE---------------------------------------- data("RawCounts_Antoszewski2022_MOUSEsub500") ## ----LoadFission, echo=TRUE, eval=TRUE------------------------------------- data("RawCounts_Leong2014_FISSIONsub500wt") ## ----LoadLeuk, echo=TRUE, eval=TRUE---------------------------------------- data("RawCounts_Schleiss2021_CLLsub500") ## ----LoadMus2, echo=TRUE, eval=TRUE---------------------------------------- data("RawCounts_Weger2021_MOUSEsub500") ## ----ColnamesExample, echo=TRUE, eval=TRUE--------------------------------- data("RawCounts_Leong2014_FISSIONsub500wt") colnames(RawCounts_Leong2014_FISSIONsub500wt) ## ----ExampleParametersData, echo=FALSE, eval=TRUE-------------------------- data("RawCounts_Leong2014_FISSIONsub500wt") ## ----ExampleParameters, echo=TRUE, eval=TRUE------------------------------- resSEexample <- DATAprepSE(RawCounts=RawCounts_Leong2014_FISSIONsub500wt, Column.gene=1, Group.position=NULL, Time.position=2, Individual.position=3) ## ----DATAprepSEmus1, echo=TRUE, eval=TRUE---------------------------------- resSEmus1500 <- DATAprepSE(RawCounts=RawCounts_Antoszewski2022_MOUSEsub500, Column.gene=1, Group.position=1, Time.position=NULL, Individual.position=2) ## ----DATAprepSEfission, echo=TRUE, eval=TRUE------------------------------- resSEfission500 <- DATAprepSE(RawCounts=RawCounts_Leong2014_FISSIONsub500wt, Column.gene=1, Group.position=NULL, Time.position=2, Individual.position=3) ## ----DATAprepSEleuk, eval=TRUE--------------------------------------------- resSEleuk500 <- DATAprepSE(RawCounts=RawCounts_Schleiss2021_CLLsub500, Column.gene=1, Group.position=2, Time.position=4, Individual.position=3) ## ----DATAprepSEmus22, eval=TRUE-------------------------------------------- resSEmus2500 <- DATAprepSE(RawCounts=RawCounts_Weger2021_MOUSEsub500, Column.gene=1, Group.position=1, Time.position=2, Individual.position=3) ## ----NormalizationMouse1, echo=TRUE, eval=TRUE----------------------------- resNORMmus1500 <- DATAnormalization(SEres=resSEmus1500, Normalization="rle", Blind.rlog.vst=FALSE, Plot.Boxplot=TRUE, Colored.By.Factors=TRUE, Color.Group=NULL, path.result=NULL) ## ----NormalizationMouseColor, eval=TRUE------------------------------------ data.col.mus50<-data.frame(Name=c("N1wtT1wt","N1haT1wt","N1haT1ko","N1wtT1ko"), Col=c("black","red","green","blue")) ## ----NormalizationFission, eval=TRUE--------------------------------------- resNORMyeast500 <- DATAnormalization(SEres=resSEfission500, Normalization="rlog", Blind.rlog.vst=FALSE, Plot.Boxplot=FALSE, Colored.By.Factors=TRUE, Color.Group=NULL, Plot.genes=FALSE, path.result=NULL) ## ----NormalizationLeukemia, eval=TRUE-------------------------------------- resNORMleuk500<-DATAnormalization(SEres=resSEleuk500, Normalization="vst", Blind.rlog.vst=FALSE, Plot.Boxplot=FALSE, Colored.By.Factors=TRUE, Color.Group = NULL, path.result=NULL) ## ----NormalizationCLLcolor, eval=TRUE-------------------------------------- data.col.Leuk<-data.frame(Name=c("NP","P"), Col=c("black","red")) ## ----NormalizationMouse2, eval=TRUE---------------------------------------- resNORMmus2500 <- DATAnormalization(SEres=resSEmus2500, Normalization="vst", Blind.rlog.vst=FALSE, Plot.Boxplot=FALSE, Colored.By.Factors=TRUE, Color.Group=NULL, path.result=NULL) ## ----NormalizationMus2color, eval=TRUE------------------------------------- data.col.Mus2 <- data.frame(Name=c("BmKo","BmWt","CrKo","CrWt"), Col=c("red","blue","orange","darkgreen")) ## ----PCAMouse1, eval=TRUE-------------------------------------------------- ResPCAMus500 <- PCAanalysis(SEresNorm=resNORMmus1500, sample.deletion=NULL, Supp.del.sample=FALSE, gene.deletion=NULL, Plot.PCA=TRUE, Mean.Accross.Time=FALSE, Color.Group = NULL, Cex.label=0.8, Cex.point=0.7, epsilon=0.2, Phi=25,Theta=140, D3.mouvement=FALSE, path.result=NULL) ## ----PCAMouseColor, eval=TRUE---------------------------------------------- data.col.mus50<-data.frame(Name=c("N1wtT1wt","N1haT1wt","N1haT1ko","N1wtT1ko"), Col=c("black","red","green","blue")) data.col.mus50 ## ----HCPCmouse1, warning=FALSE, message=FALSE, eval=TRUE------------------- ResHCPCMus500 <- HCPCanalysis(SEresNorm=resNORMmus1500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.HCPC=FALSE, Cex.label=0.8, Cex.point=0.7, epsilon=0.2, Phi=25, Theta=140, D3.mouvement=FALSE, path.result=NULL) ## ----PCAfission, warning=FALSE, message=FALSE, eval=TRUE------------------- ResPCAYeast500 <- PCAanalysis(SEresNorm=resNORMyeast500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.PCA=FALSE, Mean.Accross.Time=FALSE, Cex.label=0.8, Cex.point=0.7, epsilon=0.3, Phi=25,Theta=140, D3.mouvement=FALSE, path.result=NULL) ## ----HCPCfission, warning=FALSE, message=FALSE, eval=TRUE------------------ ResHCPCYeast500 <- HCPCanalysis(SEresNorm=resNORMyeast500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.HCPC=TRUE, Cex.label=0.9, Cex.point=0.7, epsilon=0.2, Phi=25,Theta=140, D3.mouvement=FALSE, path.result=NULL) ## ----PCALeukemia, warning=FALSE, message=FALSE, eval=TRUE------------------ ResPCALeuk500 <- PCAanalysis(SEresNorm=resNORMleuk500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.PCA=FALSE, Mean.Accross.Time=FALSE, Color.Group = NULL, Cex.label=0.9, Cex.point=0.8,epsilon=0.2, Phi=25,Theta=140, D3.mouvement=FALSE, path.result=NULL, Name.folder.pca=NULL) ## ----PCAleukColor, warning=FALSE, message=FALSE, eval=TRUE----------------- data.col.Leuk<-data.frame(Name=c("NP","P"), Col=c("black","red")) ## ----HCPCleukemia, warning=FALSE, message=FALSE, eval=TRUE----------------- ResHCPCLeuk500 <- HCPCanalysis(SEresNorm=resNORMleuk500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.HCPC=FALSE, Phi=25,Theta=140, Cex.point=0.7, epsilon=0.2, Cex.label=0.9, D3.mouvement=FALSE, path.result=NULL, Name.folder.hcpc=NULL) ## ----PCAMus2, warning=FALSE, message=FALSE, eval=TRUE---------------------- ResPCAMus2500 <- PCAanalysis(SEresNorm=resNORMmus2500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.PCA=FALSE, Mean.Accross.Time=FALSE, Color.Group=NULL, Cex.label=0.6, Cex.point=0.7, epsilon=0.2, Phi=25,Theta=140, D3.mouvement=FALSE, path.result=NULL, Name.folder.pca=NULL) ## ----PCAmus2color, warning=FALSE, message=FALSE, eval=TRUE----------------- data.col.Mus2<-data.frame(Name=c("BmKo","BmWt","CrKo","CrWt"), Col=c("red","blue","orange","darkgreen")) ## ----HCPCmus2500, warning=FALSE, message=FALSE, eval=TRUE------------------ ResHCPCMus2500 <- HCPCanalysis(SEresNorm=resNORMmus2500, gene.deletion=NULL, sample.deletion=NULL, Supp.del.sample=FALSE, Plot.HCPC=FALSE, Phi=25,Theta=140, Cex.point=0.6, epsilon=0.2, Cex.label=0.6, D3.mouvement=FALSE, path.result=NULL, Name.folder.hcpc=NULL) ## ----MfuzzFission, warning=FALSE, message=FALSE, eval=TRUE----------------- ResMfuzzYeast500 <- MFUZZanalysis(SEresNorm=resNORMyeast500, DataNumberCluster=NULL, Method="hcpc", Membership=0.5, Min.std=0.1, Plot.Mfuzz=TRUE, path.result=NULL) ## ----MfuzzLeuk, warning=FALSE, message=FALSE, eval=TRUE-------------------- ResMfuzzLeuk500 <- MFUZZanalysis(SEresNorm = resNORMleuk500, DataNumberCluster=NULL, Method="hcpc", Membership=0.7, Min.std=0.1, Plot.Mfuzz=FALSE, path.result=NULL, Name.folder.mfuzz=NULL) ## ----MfuzzMus2, warning=FALSE, message=FALSE, eval=TRUE-------------------- ResMfuzzLeuk500 <- MFUZZanalysis(SEresNorm=resNORMmus2500, DataNumberCluster=NULL, Method="hcpc", Membership=0.5, Min.std=0.1, Plot.Mfuzz=FALSE, path.result=NULL, Name.folder.mfuzz=NULL) ## ----DATAplotExpressionGenesMouse, warning=FALSE, message=FALSE, eval=TRUE---- resEVOmus1500 <- DATAplotExpressionGenes(SEresNorm=resNORMmus1500, Vector.row.gene=c(10), Color.Group=NULL, Plot.Expression=TRUE, path.result=NULL) ## ----ProfileMouseColor, warning=FALSE, message=FALSE, eval=TRUE------------ data.col.mus50<-data.frame(Name=c("N1wtT1wt","N1haT1wt","N1haT1ko","N1wtT1ko"), Col=c("black","red","green","blue")) ## ----DATAplotExpressionGenesFission, warning=FALSE, message=FALSE, eval=TRUE---- resEVOyeast500<-DATAplotExpressionGenes(SEresNorm=resNORMyeast500, Vector.row.gene=c(17), Plot.Expression=TRUE, path.result=NULL) ## ----DATAplotExpressionGenesLeukemia, warning=FALSE, message=FALSE, eval=TRUE---- resEVOleuk500 <- DATAplotExpressionGenes(SEresNorm=resNORMleuk500, Vector.row.gene=c(25), Color.Group = NULL, Plot.Expression=FALSE, path.result=NULL, Name.folder.profile=NULL) ## ----ProfileCLLcolor, warning=FALSE, message=FALSE, eval=TRUE-------------- data.col.Leuk<-data.frame(Name=c("NP","P"), Col=c("black","red")) ## ----DATAplotExpressionGenesMusBmCrKoWt, warning=FALSE, message=FALSE, eval=TRUE---- resEVOmus2500 <- DATAplotExpressionGenes(SEresNorm=resNORMmus2500, Vector.row.gene=c(17), Color.Group=NULL, Plot.Expression=FALSE, path.result=NULL) ## ----PreprocessPCAHcpcMusBmCrKoWt, warning=FALSE, message=FALSE, eval=TRUE---- data.col.MusBmCrKoWt<-data.frame(Name=c("BmKo","BmWt","CrKo","CrWt"), Col=c("black","blue","green","red")) ## ----DEmouse, warning=FALSE, message=FALSE, eval=TRUE---------------------- ResDEMus500 <- DEanalysisGlobal(SEres=resSEmus1500, pval.min=0.05, pval.vect.t=NULL, log.FC.min=1, LRT.supp.info=FALSE, Plot.DE.graph=TRUE, path.result=NULL, Name.folder.DE=NULL) # data("Results_DEanalysis_sub500") # ResDEMus500<-Results_DEanalysis_sub500$DE_Antoszewski2022_MOUSEsub500 ## ----DEresultsMouse1, warning=FALSE, message=FALSE, eval=TRUE-------------- Res.DE.results.Mus1 <- SummarizedExperiment::rowData(ResDEMus500) ## ----GlossaryMouse1, warning=FALSE, message=FALSE, eval=TRUE--------------- ResGlossary.Mus1 <- S4Vectors::metadata(ResDEMus500)$DESeq2obj$List.Glossary ## ----DEanalysisFISSION, warning=FALSE, message=FALSE, eval=TRUE------------ # DEyeast500wt <- DEanalysisGlobal(SEres=resSEfission500, # pval.min=0.05, # pval.vect.t=NULL, # log.FC.min=1, # LRT.supp.info=FALSE, # Plot.DE.graph =FALSE, # path.result=NULL, # Name.folder.DE=NULL) data("Results_DEanalysis_sub500") DEyeast500wt <- Results_DEanalysis_sub500$DE_Leong2014_FISSIONsub500wt ## ----DEresultsFission, warning=FALSE, message=FALSE, eval=TRUE------------- Res.DE.results.Fission <- SummarizedExperiment::rowData(DEyeast500wt) ## ----GlossaryFission, warning=FALSE, message=FALSE, eval=TRUE-------------- ResGlossary.Fission <- S4Vectors::metadata(DEyeast500wt)$DESeq2obj$List.Glossary ## ----DELeuk, warning=FALSE, message=FALSE, eval=TRUE----------------------- ResDELeuk500 <- DEanalysisGlobal(SEres=resSEleuk500, pval.min=0.05, pval.vect.t=NULL, log.FC.min=1, LRT.supp.info=FALSE, Plot.DE.graph =TRUE, path.result=NULL, Name.folder.DE=NULL) # data("Results_DEanalysis_sub500") # ResDELeuk500<-Results_DEanalysis_sub500$DE_Schleiss2021_CLLsub500 ## ----DEresultsLeukemia, warning=FALSE, message=FALSE, eval=TRUE------------ Res.DE.results.Leuk <- SummarizedExperiment::rowData(ResDELeuk500) ## ----GlossaryLeukemia, warning=FALSE, message=FALSE, eval=TRUE------------- ResGlossary.Leuk <- S4Vectors::metadata(ResDELeuk500)$DESeq2obj$List.Glossary ## ----UsbMusBmCrKoWt, warning=FALSE, message=FALSE, eval=TRUE--------------- Sub3bc3T <- RawCounts_Weger2021_MOUSEsub500[, seq_len(73)] SelectTime <- grep("_t0_", colnames(Sub3bc3T)) SelectTime <- c(SelectTime, grep("_t1_", colnames(Sub3bc3T))) SelectTime <- c(SelectTime, grep("_t2_", colnames(Sub3bc3T))) Sub3bc3T <- Sub3bc3T[, c(1, SelectTime)] resSEmus25003b3t <- DATAprepSE(RawCounts=Sub3bc3T, Column.gene=1, Group.position=1, Time.position=2, Individual.position=3) ## ----DEMusBmCrKoWt, warning=FALSE, message=FALSE, eval=TRUE---------------- ResDEMusBmCrKoWt500<-DEanalysisGlobal(SEres=resSEmus25003b3t, pval.min=0.05, pval.vect.t=NULL, log.FC.min=1, LRT.supp.info=FALSE, Plot.DE.graph=FALSE, path.result=NULL, Name.folder.DE=NULL) ## ----VolcanoMAMus1, warning=FALSE, message=FALSE, eval=TRUE---------------- resVolcanoMAMouse <- DEplotVolcanoMA(SEresDE=ResDEMus500, NbGene.plotted=2, SizeLabel=3, Display.plots=TRUE, Save.plots=FALSE) ## ----HeatmapsMus1, warning=FALSE, message=FALSE, eval=TRUE----------------- resplotHeatmapMus <- DEplotHeatmaps(SEresDE=ResDEMus500, ColumnsCriteria=2,#c(2,4), Set.Operation="union", NbGene.analysis=20, SizeLabelRows=5, SizeLabelCols=5, Display.plots=TRUE, Save.plots=FALSE) ## ----VolcanoMA_FISSION, warning=FALSE, message=FALSE, eval=TRUE------------ resVolcanoMAFission <- DEplotVolcanoMA(SEresDE=DEyeast500wt, NbGene.plotted=2, SizeLabel=3, Display.plots=TRUE, Save.plots=TRUE) ## ----Heatmaps_FISSION, warning=FALSE, message=FALSE, eval=TRUE------------- resplotHeatmapFission <- DEplotHeatmaps(SEresDE=DEyeast500wt, ColumnsCriteria=2, Set.Operation="union", NbGene.analysis=20, Color.Group=NULL, SizeLabelRows=5, SizeLabelCols=5, Display.plots=TRUE, Save.plots=FALSE) ## ----VolcanoMA_CLL, warning=FALSE, message=FALSE, eval=TRUE---------------- resVolcanoMACLL<-DEplotVolcanoMA(SEresDE=ResDELeuk500, NbGene.plotted=2, SizeLabel=3, Display.plots=FALSE, Save.plots=FALSE) ## ----Heatmaps_CCL, warning=FALSE, message=FALSE, eval=TRUE----------------- resplotHeatmapCLL<-DEplotHeatmaps(SEresDE=ResDELeuk500, ColumnsCriteria=c(12, 13), Set.Operation="union", NbGene.analysis=20, SizeLabelRows=5, SizeLabelCols=5, Display.plots=FALSE, Save.plots=FALSE) ## ----VolcanoMA_Mouse2, warning=FALSE, message=FALSE, eval=TRUE------------- resVolcanoMAMouse2<-DEplotVolcanoMA(SEresDE=ResDEMusBmCrKoWt500, NbGene.plotted=2, SizeLabel=3, Display.plots=FALSE, Save.plots=FALSE) ## ----Heatmaps_Mouse2, warning=FALSE, message=FALSE, eval=TRUE-------------- resplotHeatmapMouse2<-DEplotHeatmaps(SEresDE=ResDEMusBmCrKoWt500, ColumnsCriteria=2:5, Set.Operation="union", NbGene.analysis=20, SizeLabelRows=5, SizeLabelCols=5, Display.plots=FALSE, Save.plots=FALSE) ## ----GSEAquickAnalysis_Mus, warning=FALSE, message=FALSE, eval=TRUE-------- resGSEAgprofiler2Mus<-GSEAQuickAnalysis(Internect.Connection=FALSE, SEresDE=ResDEMus500, ColumnsCriteria=2, ColumnsLog2ordered=NULL, Set.Operation="union", Organism="mmusculus", MaxNumberGO=10, Background=FALSE, Display.plots=FALSE, Save.plots=FALSE) # # head(4Vectors::metadata(resGSEAgprofiler2Mus)$Rgprofiler2$GSEAresults) ## ----GSEAprepro_Mus1, warning=FALSE, message=FALSE, eval=TRUE-------------- resGSEApreprocessingFission<-GSEApreprocessing(SEresDE=ResDEMus500, ColumnsCriteria=2, Set.Operation="union", Rnk.files=FALSE, Save.files=FALSE) ## ----GSEAquickAnalysis_Fission, warning=FALSE, message=FALSE, eval=TRUE---- resGSEAgprofiler2Fission<-GSEAQuickAnalysis(Internect.Connection=FALSE, SEresDE=DEyeast500wt, ColumnsCriteria=2, ColumnsLog2ordered=NULL, Set.Operation="union", Organism="spombe", MaxNumberGO=20, Background=FALSE, Display.plots=FALSE, Save.plots=FALSE) # # head(resGSEAgprofiler2Fission$GSEAresults) ## ----GSEAprepro_Fission, warning=FALSE, message=FALSE, eval=TRUE----------- resGSEApreprocessingFission<-GSEApreprocessing(SEresDE=DEyeast500wt, ColumnsCriteria=2, Set.Operation="union", Rnk.files=FALSE, Save.files=FALSE) ## ----GSEAquickAnalysis_CLL, warning=FALSE, message=FALSE, eval=TRUE-------- resGSEAgprofiler2Leuk<-GSEAQuickAnalysis(Internect.Connection=FALSE, SEresDE=ResDELeuk500, ColumnsCriteria=c(12,13), ColumnsLog2ordered=NULL, Set.Operation="union", Organism="hsapiens", MaxNumberGO=20, Background=FALSE, Display.plots=FALSE, Save.plots=FALSE) # # head(resGSEAgprofiler2Leuk$GSEAresults) ## ----GSEAprepro_CLL, warning=FALSE, message=FALSE, eval=TRUE--------------- resGSEApreprocessingLeuk<-GSEApreprocessing(SEresDE=ResDELeuk500, ColumnsCriteria=c(12,13), Set.Operation="union", Rnk.files=FALSE, Save.files=FALSE) ## ----GSEAquickAnalysis_Mouse2, warning=FALSE, message=FALSE, eval=TRUE----- resGSEAgprofiler2Mouse2<-GSEAQuickAnalysis(Internect.Connection=FALSE, SEresDE=ResDEMusBmCrKoWt500, ColumnsCriteria=2:5, ColumnsLog2ordered=NULL, Set.Operation="union", Organism="mmusculus", MaxNumberGO=20, Background=FALSE, Display.plots=FALSE, Save.plots=FALSE) # # head(resGSEAgprofiler2Mouse2$GSEAresults) ## ----GSEAprepro_Mouse2, warning=FALSE, message=FALSE, eval=TRUE------------ resGSEApreprocessing<-GSEApreprocessing(SEresDE=ResDEMusBmCrKoWt500, ColumnsCriteria=2:5, Set.Operation="union", Rnk.files=FALSE, Save.files=TRUE) ## ----sessionInfo, echo=FALSE, results="asis"------------------------------- utils::toLatex(sessionInfo())