GetPPMat: Posterior Probability of Transcripts

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

Description

'GetPPMat' generates the Posterior Probability of being each pattern of each transcript based on the EBTest output.

Usage

GetPPMat(EBout)

Arguments

EBout

The output of EBTest function.

Value

The poster probabilities of being EE (first column) and DE (second column).

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(500:550),]
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)
str(PP)
head(PP)

EBSeq documentation built on Nov. 8, 2020, 6:52 p.m.