crit_fun: Calculate the soft threshold for a target FDR

In lengning/EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

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)]

lengning/EBSeq documentation built on May 21, 2019, 4:02 a.m.