estimatePs {edgeR} | R Documentation |
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)
estimatePs(object, r, tol = 1e-10, maxit = 30)
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 |
list with elements p.common
(vector giving overall proportion for each tag), p.group
(matrix with columns giving estimates of proportions for different groups)
Mark Robinson, Davis McCarthy
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)