## ----setup, echo=FALSE, results="hide"----------------------------------- knitr::opts_chunk$set(tidy=FALSE, cache=TRUE, dev="png", message=FALSE, error=FALSE, warning=TRUE) ## ----bioC, eval=FALSE---------------------------------------------------- # ## try http:// if https:// URLs are not supported # if (!require("BiocManager")) # install.packages("BiocManager") # BiocManager::install("NBSplice", version="devel") ## ----expMat built, eval=FALSE-------------------------------------------- # fileNames<-c(paste(rep("C1R",4), 1:4,"/abundance.tsv", sep=""), # paste(rep("C2R",4), 1:4,"/abundance.tsv", sep="")) # # myInfo<-lapply(seq_along(fileNames), function(x){ # quant<-read.delim(fileNames[x], header = TRUE) # expression<-quant[,"est_counts"] # return(expression) # }) # # Adding the isoform IDS as row names # isoform_id<-read.delim(fileNames[x], header = TRUE)[,"target_id"] # expressionMatrix<-(do.call(cbind, myInfo)) # rownames(expressionMatrix)<-isoform_id # # Adding the samples names as column names # colnames(expressionMatrix)<-c(paste(rep("C1R",4), 1:4, sep=""), # paste(rep("C2R",4), 1:4, sep="")) ## ----expMat, eval=TRUE--------------------------------------------------- data(isoCounts, package="NBSplice") head(isoCounts) dim(isoCounts) ## ----geneIsoMat, eval=TRUE----------------------------------------------- data(geneIso, package="NBSplice") head(geneIso) dim(geneIso) ## ----designMat, eval=TRUE------------------------------------------------ designMatrix<-data.frame(sample=c(paste(rep("C1R", 4), 1:4, sep=""), paste(rep("C2R", 4), 1:4, sep="")), condition=c(rep( "Normal", 4), rep("Tumor", 4))) rownames(designMatrix)<-designMatrix[,"sample"] designMatrix ## ----colData, eval=TRUE-------------------------------------------------- colName<-"condition" levels(designMatrix[,colName]) ## ----objectBuild, eval=TRUE---------------------------------------------- library(NBSplice) myIsoDataSet<-IsoDataSet(isoCounts, designMatrix, colName, geneIso) ## ----objectInsp, eval=TRUE----------------------------------------------- show(myIsoDataSet) head(isoCounts(myIsoDataSet)) ## ----lowExp, eval=TRUE--------------------------------------------------- myIsoDataSet<-buildLowExpIdx(myIsoDataSet, colName, ratioThres = 0.01, countThres = 1) ## ----NBTest, eval=TRUE--------------------------------------------------- myDSResults<-NBTest(myIsoDataSet, colName, test="F") ## ----object loading2, echo=FALSE, eval=TRUE, results="hide"-------------- data(myDSResults, package="NBSplice") ## ----NBRes, eval=TRUE---------------------------------------------------- head(lowExpIndex(myDSResults)) contrast(myDSResults) head(results(myDSResults)) ## ----lowExpRes, eval=TRUE------------------------------------------------ head(results(myDSResults, filter = FALSE)) ## ----getDSGe, eval=TRUE-------------------------------------------------- mySignificantRes<-GetDSResults(myDSResults) head(mySignificantRes) dim(mySignificantRes) myDSGenes<-GetDSGenes(myDSResults) head(myDSGenes) length(myDSGenes) ## ----plotD, eval=TRUE---------------------------------------------------- plotRatiosDisp(myDSResults) ## ----plotv, eval=TRUE---------------------------------------------------- plotVolcano(myDSResults) ## ----plotGene, eval=TRUE------------------------------------------------- ## Select the first differentially spliced gene gene<-GetDSGenes(myDSResults)[1] GetGeneResults(myDSResults, gene) plotGeneResults(myDSResults, gene) ## ----plotGene2, eval=TRUE------------------------------------------------ ## Keeping non-reliable and non-significant isoforms plotGeneResults(myDSResults, gene, filterLowExpIso = FALSE, filterNotSignificant = FALSE) ## ----sessionInfo--------------------------------------------------------- sessionInfo()