GetAllPaths {EBSeqHMM} | R Documentation |
Obtain all possible gene paths for an RNA-seq experiments with ordered conditions
GetAllPaths(EBSeqHMMOut, OnlyDynamic=TRUE)
EBSeqHMMOut |
output from EBSeqHMMTest function |
OnlyDynamic |
if specifies as TRUE, only dynamic paths will be shown |
GetAllPaths() function may be used to generate all possible expression paths of a particular design.
output: a vector of paths. For example, Up-Up-Up-Up, Up-Up-EE-EE, Up-Down-Up-EE, etc.
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) AllPaths <- GetAllPaths(EBSeqHMMGeneOut)