Displaying 1 result from an estimated 1 matches for "possalleles".
2012 Apr 26
0
Problem with constrOptim when hitting boundary
...2.15.0
My function:
eventTiming<-function(x,m,history, exactAllele=FALSE,normCont=0,verbose=FALSE,coverageCutoff=1,minMutations=10){
A<-history
if(is.null(dim(A))) stop("'history' should be a matrix of size nCopies x (nEvents +1)")
nCopies<-nrow(A)
K<-ncol(A)-1
possAlleles<-(1:nCopies)/nCopies*(1-normCont)
nMuts<-length(x)
if(length(m)!=nMuts) stop("x and m must be of same length")
if(coverageCutoff<1) stop("coverageCutoff must be at least 1")
if(any(m<coverageCutoff)){
if(verbose) warning("some mutations have no reads, will...