newReadCountSet: Generate a new ReadCountSet object

In sunlightwang/SeqGSEA: Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing

Description

This is a internal function to generate a new ReadCountSet object.

Usage

newReadCountSet(readCounts, exonIDs, geneIDs)

Arguments

readCounts	a data frame, read counts for each exon of each samples. Must have colnames, which indicate the label of samples.
exonIDs	a character vector indicating exon IDs.
geneIDs	a character vector indicating gene IDs.

Value

A object of the ReadCountSet class.

Author(s)

Xi Wang, [e-mail]

See Also

loadExonCountData, ReadCountSet-class

Examples

rcounts <- cbind(t(sapply(1:10, function(x) {rnbinom(5, size=10, prob=runif(1))} ) ) , 
                 t(sapply(1:10, function(x) {rnbinom(5, size=10, prob=runif(1))} ) ) )
colnames(rcounts) <- c(paste("S", 1:5, sep=""), paste("C", 1:5, sep="")) 
geneIDs <- c(rep("G1", 4), rep("G2", 6))
exonIDs <- c(paste("E", 1:4, sep=""), paste("E", 1:6, sep=""))
## 
RCS <- newReadCountSet(rcounts, exonIDs, geneIDs)
RCS 
## End

sunlightwang/SeqGSEA documentation built on Dec. 5, 2020, 5:52 p.m.