EBSeq (version 1.12.0)

LogN: The function to run EM (one round) algorithm for the NB-beta model.

Description

'LogN' specifies the function to run (one round of) the EM algorithm for the NB-beta model.

Usage

LogN(Input, InputSP, EmpiricalR, EmpiricalRSP, NumOfEachGroup, 
	AlphaIn, BetaIn, PIn, NoneZeroLength)

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.

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 = LogN(Input, list(Input[,1:5], Input[,6:10]),
#	RIn, list(RIn[,1:5], RIn[,6:10]), 
#	10, .6, .7, .3, 1)