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(y1, y2, lib.size1, lib.size2, r, tol = 1e-10, maxit = 30)
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 |
list with elements p
(overall proportion), p1
(estimates for first group), p2
(estimates for second group)
Mark Robinson
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)