GetDECalls {EBSeqHMM} | R Documentation

## Obtain DE gene/isoform list at a certain FDR

### Description

Obtain DE gene/isoform list at a certain FDR

### Usage

    GetDECalls(EBSeqHMMOut,FDR=.05)

### Arguments

`EBSeqHMMOut` | output from EBSeqHMMTest function
`FDR` | Target FDR; default is 0.05

### Details

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.

### Value

a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs;

### Note

Output: output a list of genes that are DE in at least one condition in an RNA-seq experiment with multiple ordered conditions

### 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)
    GeneDECalls <- GetDECalls(EBSeqHMMGeneOut, FDR=.05)

[Package EBSeqHMM version 1.14.0 Index]