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

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

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.

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

wiscstatman/EBSeq documentation built on June 3, 2023, 7:34 a.m.