GetPP: Generate the Posterior Probability of each transcript.
In EBSeq: An R package for gene and isoform differential expression analysis of RNA-seq data

Description Usage Arguments Value Author(s) References See Also Examples

'GetPP' generates the Posterior Probability of being DE of each transcript based on the EBTest output.

1	GetPP(EBout)

EBout

The output of EBTest function.

The poster probabilities of being DE.

Ning Leng

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)

GetPPMat

data(GeneMat)
GeneMat.small = GeneMat[c(1:10,500:550),]
Sizes = MedianNorm(GeneMat.small)
EBOut = EBTest(Data = GeneMat.small,
	Conditions = as.factor(rep(c("C1","C2"), each=5)),
	sizeFactors = Sizes, maxround = 5)
PPDE = GetPP(EBOut)
str(PPDE)
head(PPDE)

Loading required package: blockmodeling
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

Loading required package: testthat
iteration 1 done 

time 0.18 

iteration 2 done 

time 0.08 

iteration 3 done 

time 0.05 

iteration 4 done 

time 0.06 

iteration 5 done 

time 0.05 

 Named num [1:61] 1 1 1 1 1 ...
 - attr(*, "names")= chr [1:61] "Gene_1" "Gene_2" "Gene_3" "Gene_4" ...
Gene_1 Gene_2 Gene_3 Gene_4 Gene_5 Gene_6 
     1      1      1      1      1      1