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(object, r, tol = 1e-10, maxit = 30) 

Arguments

object list containing the raw data with elements data (table of counts), group (vector indicating group) and lib.size (vector of library sizes)
r size parameter of negative binomial
tol tolerance between iterations
maxit maximum number of iterations

Value

list with elements p.common (vector giving overall proportion for each tag), p.group (matrix with columns giving estimates of proportions for different groups)

Author(s)

Mark Robinson, Davis McCarthy

Examples

set.seed(0)
y<-matrix(rnbinom(40,size=1,mu=10),ncol=4)
d<-DGEList(data=y,group=rep(1:2,each=2),lib.size=rep(c(1000:1001),2))
ps<-estimatePs(d,r=1)

[Package edgeR version 1.2.4 Index]