GetConfidentCalls {EBSeqHMM} | R Documentation

## Obtain confident gene calls for classifying genes into expression paths

### Description

Obtain confident gene calls for classifying genes into expression paths

### Usage

    GetConfidentCalls(EBSeqHMMOut, FDR=.05, cutoff=0.5, OnlyDynamic=TRUE,Paths=NULL)

### Arguments

`EBSeqHMMOut` | output from EBSeqHMMTest function
`FDR` | Target FDR, default is 0.05.
`cutoff` | cutoff to use for defining a confident call. Genes with PP_path greater or equal to cutoff will be called as a confident call. Default is 0.5.
`OnlyDynamic` | if specifies as T, only dynamic paths will be shown
`Paths` | paths that are of interest. Default is NULL. If it is not specified, all possible paths will be considered.

### Details

Function GetConfidentCalls() 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. To further choose genes/isoforms with high posterior probability of being its most likely path, the user may specify the option cutoff (default is 0.5). Then genes or isoforms with PP(most likely path ) > = 0.5 will be selected

### Value

Overall: a list of genes/isoforms that are identified as DE under the target FDR, shown are their names and PPs; EachPath: a list object, each sublist contains confident calls (genes/isoforms) that have PP(path)>=cutoff for a particular expression path, shown are their names and PPs; NumEach: length of each sublist in EachPath. EachPathName: gene/isoform names in each of the sublists in EachPath

### Note

Output: output a list of genes that are classified to a expression path as a confident assignment.

### 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)
    GeneConfCalls <- GetConfidentCalls(EBSeqHMMGeneOut, FDR=.05,cutoff=.5, OnlyDynamic=TRUE)

[Package EBSeqHMM version 1.22.0 Index]