crit_fun {EBSeq} | R Documentation

## Calculate the soft threshold for a target FDR

### Description

'crit_fun' calculates the soft threshold for a target FDR.

### Usage

    crit_fun(PPEE, thre)

### Arguments

`PPEE` | The posterior probabilities of being EE.
`thre` | The target FDR.

### Details

Regarding a target FDR alpha, both hard threshold and soft threshold could be used. If the hard threshold is preferred, user could simply take the transcripts with PP(DE) greater than (1-alpha). Using the hard threshold, any DE transcript in the list is with FDR <= alpha.

If the soft threshold is preferred, user could take the transcripts with PP(DE) greater than crit_fun(PPEE, alpha). Using the soft threshold, the list of DE transcripts is with average FDR alpha.

### Value

The adjusted FDR threshold of target FDR.

### Author(s)

Ning Leng

### References

Ning Leng, John A. Dawson, James A. Thomson, Victor Ruotti, Anna I. Rissman, Bart M.G. Smits, Jill D. Haag, Michael N. Gould, Ron M. Stewart, and Christina Kendziorski. EBSeq: An empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics (2013)

### Examples

    data(GeneMat)
    GeneMat.small = GeneMat[c(1:10, 500:600),]
    Sizes = MedianNorm(GeneMat.small)
    EBOut = EBTest(Data = GeneMat.small,
    	Conditions = as.factor(rep(c("C1","C2"), each=5)),
    	sizeFactors = Sizes, maxround = 5)
    PP = GetPPMat(EBOut)
    DEfound = rownames(PP)[which(PP[,"PPDE"] >= 0.95)]
    str(DEfound)

    SoftThre = crit_fun(PP[,"PPEE"], 0.05)
    DEfound_soft = rownames(PP)[which(PP[,"PPDE"] >= SoftThre)]

[Package EBSeq version 1.30.0 Index]