GetDECalls {EBSeqHMM} | R Documentation |
Obtain DE gene/isoform list at a certain FDR
GetDECalls(EBSeqHMMOut,FDR=.05)
EBSeqHMMOut |
output from EBSeqHMMTest function |
FDR |
Target FDR; default is 0.05 |
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.
a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs;
Output: output a list of genes that are DE in at least one condition in an RNA-seq experiment with multiple ordered conditions
Ning Leng
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)