LogNMulti: EM algorithm for the NB-beta model in the multiple condition...

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

Description

'LogNMulti' specifies the function to run (one round of) the EM algorithm for the NB-beta model in the multiple condition test.

Usage

LogNMulti(Input, InputSP, EmpiricalR, EmpiricalRSP, 
	NumOfEachGroup, AlphaIn, BetaIn, PIn, 
	NoneZeroLength, AllParti, Conditions)

Arguments

Input, InputSP	The expressions among all the samples.
NumOfEachGroup	Number of genes in each Ng group.
AlphaIn, PIn, BetaIn, EmpiricalR, EmpiricalRSP	The parameters from the last EM step.
NoneZeroLength	Number of Ng groups.
AllParti	The patterns of interests.
Conditions	The condition assignment for each sample.

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

#

#Input = matrix(rnorm(100,100,1),ncol=10)
#rownames(Input) = paste("g",1:10)
#RIn = matrix(rnorm(100,200,1), ncol=10)
#res = LogNMulti(Input, list(Input[,1:5], Input[,6:10]),
#	RIn, list(RIn[,1:5], RIn[,6:10]), 10, .6, .7, 
#	c(.3,.7), 1, rbind(c(1,1), c(1,2)), 
#	as.factor(rep(c("C1","C2"), each=5)))

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