EBSeqHMM (version 1.6.0)

GetDECalls: Obtain DE gene/isoform list at a certain FDR

Description

Obtain DE gene/isoform list at a certain FDR

Usage

GetDECalls(EBSeqHMMOut,FDR=.05)

Arguments

EBSeqHMMOut

output from EBSeqHMMTest function

FDR

Target FDR; default is 0.05

Value

a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs;

Details

Function GetDECalls() can be used to obtain a list of DE genes/isoforms with user specific cutoffs. To obtain a list of DE genes/isoforms with a target FDR alpha, the user may specify FDR=alpha.

Examples

data(GeneExampleData)
CondVector <- rep(paste("t",1:5,sep=""),each=3)
Conditions <- factor(CondVector, levels=c("t1","t2","t3","t4","t5"))
Sizes <- MedianNorm(GeneExampleData)
EBSeqHMMGeneOut <- EBSeqHMMTest(Data=GeneExampleData, sizeFactors=Sizes, Conditions=Conditions,
          UpdateRd=2)
GeneDECalls <- GetDECalls(EBSeqHMMGeneOut, FDR=.05)