Displaying 1 result from an estimated 1 matches for "nbelowcutoff".
2012 Apr 26
0
Problem with constrOptim when hitting boundary
...ies*(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 be ignored")
nBelowCutoff<-length(which(m<coverageCutoff))
nZero<-length(which(m==0))
x<-x[which(m>=coverageCutoff)]
m<-m[which(m>=coverageCutoff)]
}
else{
nBelowCutoff<-0
nZero<-0
}
if(length(m)<minMutations){
if(length(normCont)>0){
if(length(possAlleles)!=K+1) stop(&quo...