InterestResult {IntEREst} | R Documentation |
Calls the constructors and creates a SummarizedExperiment
object.
For more information on the resulted object and the class see
SummarizedExperiment-class
.
InterestResult(resultFiles=c(), counts, scaledRetention, scaleLength, scaleFragment, sampleAnnotation, rowData)
resultFiles |
Vector of link to the result files of |
counts |
Numeric Matrix that includes the read counts. |
scaledRetention |
Matrix that includes the scaled retention values. |
scaleLength |
Logical value, indicating whether the intron/exon retention levels are scaled to the length of the introns/exons. |
scaleFragment |
Logical value, indicating whether the intron/exon retention levels are scaled to the fragments mapped to the genes. |
sampleAnnotation |
Data frame with the row-size equal to the size of |
rowData |
Data frame with Intron/Exon annotations and read count and scaled retention values for each sample. |
Returns an object of class SummarizedExperiment
.
Ali Oghabian
SummarizedExperiment-class
attributes
addAnnotation
counts-method
plot-method
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)) InterestResultObj<- InterestResult( resultFiles=paste("file",1:4, sep="_"), rowData= interestDat[ , -c(readFreqColIndex, scaledRetentionColIndex)], counts= frqTmp, scaledRetention= scalRetTmp, scaleLength=TRUE, scaleFragment=FALSE, sampleAnnotation=data.frame( sampleName=paste("sam",1:4, sep=""), gender=c("M","M","F","F"), row.names=paste("sam", 1:4, sep="") ) ) # View object InterestResultObj