GetMultiPP: Posterior Probability of Each Transcript

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

Description

'GetMultiPP' generates the Posterior Probability of being each pattern of each transcript based on the EBMultiTest output.

Usage

GetMultiPP(EBout)

Arguments

EBout

The output of EBMultiTest function.

Value

PP	The poster probabilities of being each pattern.
MAP	Gives the most likely pattern.
Patterns	The Patterns.

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)

See Also

GetPPMat

Examples

data(MultiGeneMat)
MultiGeneMat.small = MultiGeneMat[201:210,]

Conditions = c("C1","C1","C2","C2","C3","C3")
PosParti = GetPatterns(Conditions)
Parti = PosParti[-3,]
MultiSize = MedianNorm(MultiGeneMat.small)

MultiOut = EBMultiTest(MultiGeneMat.small, 
	NgVector=NULL, Conditions=Conditions, 
	AllParti=Parti, sizeFactors=MultiSize, 
	maxround=5)
MultiPP = GetMultiPP(MultiOut)

Example output

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 0.81 

iteration 2 done 

time 0.82 

iteration 3 done 

time 0.45 

iteration 4 done 

time 0.85 

iteration 5 done 

time 0.39 

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