subInterestResult {IntEREst} | R Documentation |
Build a new object using subset of data in an SummarizedExperiment
object.
subInterestResult(x, selectRow, selectCol, sampleAnnoCol, sampleAnnotation=c())
x |
Object of type |
selectRow |
Numeric or TRUE/FALSE Vector indicating what rows to extract. |
selectCol |
A vector with Numeric values, character strings (sample names) or TRUE/FALSE Vector indicating what columns to extract. |
sampleAnnoCol |
Which colummn of |
sampleAnnotation |
Vector including the annotations to consider for subset data extraction. They
should be present in the |
An object of calss SummarizedExperiment
.
Ali Oghabian
geneId<- paste("gene", c(rep(1,7), rep(2,7), rep(3,7), rep(4,7)), sep="_") readCnt1<- sample(1:100, 28) readCnt2<- sample(1:100, 28) readCnt3<- sample(1:100, 28) readCnt4<- sample(1:100, 28) 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"),3),"exon"),4), int_ex_num= rep(c(1,1,2,2,3,3,4),4), int_type=rep(c(NA,"U2",NA,"U12",NA,"U2",NA),4), strand=rep("*",28), 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)) samNames<-paste("sam", 1:4, sep="") frqTmp<-as.matrix(interestDat[, readFreqColIndex]) sclTmp<-as.matrix(interestDat[, scaledRetentionColIndex]) colnames(frqTmp)<- samNames colnames(sclTmp)<- samNames interestResObj<- InterestResult( resultFiles=paste("file",1:4, sep="_"), rowData= interestDat[, -c(readFreqColIndex, scaledRetentionColIndex)], counts= frqTmp, scaledRetention= sclTmp , scaleLength=TRUE, scaleFragment=FALSE, sampleAnnotation=data.frame( sampleName=paste("sam",1:4, sep=""), gender=c("M","M","F","F"), health=c("healthy","unhealthy","healthy","unhealthy"), row.names=samNames ) ) #Build new object newObj<- subInterestResult(interestResObj, selectRow=1:20) #View newObj print(newObj)