mergeInterestResult {IntEREst} | R Documentation |
Build a new object bu merging data of two SummarizedExperiment
objects.
mergeInterestResult(x, y)
x |
Object of type |
y |
Object of type |
An object of calss SummarizedExperiment
.
Ali Oghabian
geneId<- paste("gene", c(rep(1,5), rep(2,5), rep(3,5), rep(4,5)), sep="_") readCnt1<- sample(1:100, 20) readCnt2<- sample(1:100, 20) readCnt3<- sample(1:100, 20) readCnt4<- sample(1:100, 20) fpkm1<- readCnt1/(tapply(readCnt1, geneId, sum))[geneId] fpkm2<- readCnt2/(tapply(readCnt2, geneId, sum))[geneId] fpkm3<- readCnt3/(tapply(readCnt3, geneId, sum))[geneId] fpkm4<- readCnt4/(tapply(readCnt4, geneId, sum))[geneId] # Creating object using test data interestDat<- data.frame( int_ex=rep(c(rep(c("exon","intron"),2),"exon"),4), int_ex_num= rep(c(1,1,2,2,3),4), gene_id= geneId, sam1_readCnt=readCnt1, sam2_readCnt=readCnt2, sam3_readCnt=readCnt3, sam4_readCnt=readCnt4, sam1_fpkm=fpkm1, sam2_fpkm=fpkm2, sam3_fpkm=fpkm3, sam4_fpkm=fpkm4 ) readFreqColIndex<- grep("_readCnt$",colnames(interestDat)) scaledRetentionColIndex<- grep("_fpkm$",colnames(interestDat)) scalRetTmp<- as.matrix(interestDat[ ,scaledRetentionColIndex]) colnames(scalRetTmp)<-gsub("_fpkm$","", colnames(scalRetTmp)) frqTmp<- as.matrix(interestDat[ ,readFreqColIndex]) colnames(frqTmp)<-gsub("_readCnt$","", colnames(frqTmp)) #Object including data for Males interestResObjM<-InterestResult( resultFiles=paste("file",1:2, sep="_"), rowData= interestDat[, -c(readFreqColIndex, scaledRetentionColIndex)], counts= frqTmp[,1:2], scaledRetention= scalRetTmp[,1:2], scaleLength=TRUE, scaleFragment=FALSE, sampleAnnotation=data.frame( sampleName=paste("sam",1:2, sep=""), gender=c("M","M"), health=c("healthy","unhealthy"), row.names=paste("sam", 1:2, sep="") ) ) #Object including data for Females interestResObjF<-InterestResult( resultFiles=paste("file",3:4, sep="_"), rowData= interestDat[, -c(readFreqColIndex, scaledRetentionColIndex)], counts= frqTmp[,3:4], scaledRetention= scalRetTmp[,3:4], scaleLength=TRUE, scaleFragment=FALSE, sampleAnnotation=data.frame( sampleName=paste("sam",3:4, sep=""), gender=c("F","F"), health=c("healthy","unhealthy"), row.names=paste("sam", 3:4, sep="") ) ) #Build new object newObj<- mergeInterestResult(interestResObjM, interestResObjF) #View newObj print(newObj)