GetMultiPP: Posterior Probability of Each Transcript

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

View source: R/GetMultiPP.R

Description

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

Usage

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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

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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.