Description Usage Arguments Details Value Author(s) Examples
Obtain all possible gene paths for an RNA-seq experiments with ordered conditions
1 | GetAllPaths(EBSeqHMMOut, OnlyDynamic=TRUE)
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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
1 2 3 4 5 6 7 | 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)
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