EBSeqHMM (version 1.6.0)

GetAllPaths: Obtain all possible gene paths for an RNA-seq experiments with ordered conditions

Description

Obtain all possible gene paths for an RNA-seq experiments with ordered conditions

Usage

GetAllPaths(EBSeqHMMOut, OnlyDynamic=TRUE)

Arguments

EBSeqHMMOut

output from EBSeqHMMTest function

OnlyDynamic

if specifies as TRUE, only dynamic paths will be shown

Value

output: a vector of paths. For example, Up-Up-Up-Up, Up-Up-EE-EE, Up-Down-Up-EE, etc.

Details

GetAllPaths() function may be used to generate all possible expression paths of a particular design.

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)
AllPaths <- GetAllPaths(EBSeqHMMGeneOut)