GetAllPaths {EBSeqHMM} | R Documentation

## 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

### Details

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

### Value

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

### Author(s)

Ning Leng

### 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)

[Package EBSeqHMM version 1.21.0 Index]