estimatePs {edgeR}R Documentation

Estimate expression proportions

Description

Estimate expression proportions (maximum likelihood with size fixed) based on negative binomial for each tag and sample group (only 2 groups implemented at this point)

Usage

 
estimatePs(y1, y2, lib.size1, lib.size2, r, tol = 1e-10, maxit = 30) 

Arguments

y1 matrix of counts for first group
y2 matrix of counts for second group
lib.size1 vector of library sizes for first group
lib.size2 vector of library sizes for second group
r size parameter of negative binomial
tol tolerance between iterations
maxit maximum number of iterations

Value

list with elements p (overall proportion), p1 (estimates for first group), p2 (estimates for second group)

Author(s)

Mark Robinson

Examples

y1<-matrix(rnbinom(10,size=1,mu=10),nrow=5)
y2<-matrix(rnbinom(10,size=1,mu=5),nrow=5)
ps<-estimatePs(y1,y2,c(1000,1001),c(1000,1001),r=1)

[Package edgeR version 1.0.4 Index]