R/read.snv.context.R

In rvalieris/signeR: Empirical Bayesian approach to mutational signature discovery

read.snv.context<-function(stvet){
    if(length(stvet)==96){
        triplets<-c()
        mutations<-c()
        for (st in stvet){
            if (grepl("[ACGT]{3,3}",st,ignore.case=TRUE,perl=TRUE)){
                strt<-regexpr("[ACGT]{3,3}",st)[[1]]
                trivet<-strsplit(st,"")[[1]][strt:(strt+2)]
                triplet<-paste(trivet,collapse="")
                st<-sub(triplet,"",st,ignore.case=TRUE)
                st<-sub(trivet[2],"",st,ignore.case=TRUE)
                strt<-regexpr("[ACGT]",st,ignore.case=TRUE)[[1]]
                newbase<-strsplit(st,"")[[1]][strt]
                mut<-paste(trivet[2],newbase,sep=">")
            }else if(grepl("[ACTG]>[ACTG]",st,ignore.case=TRUE,perl=TRUE)){
                strt<-regexpr("[ACTG]>[ACTG]",st,ignore.case=TRUE)[[1]]
                mutvet<-strsplit(st,"")[[1]][strt:(strt+2)]
                mut<-paste(mutvet,collapse="")
                st<-sub(mut,"",st,ignore.case=TRUE)
                splitvet<-strsplit(st,"")[[1]]
                splitvet<-splitvet[splitvet %in% c("A","C","G","T","a","c","g","t")]
                firstbase<-splitvet[1]
                lastbase<-splitvet[2]
                triplet<-paste(c(firstbase,mutvet[1],lastbase),collapse="")
            }else if (grepl("[ACTG]\\.[ACTG]",st,ignore.case=TRUE,perl=TRUE)){
                strt<-regexpr("[ACTG]\\.[ACTG]",st,ignore.case=TRUE)[[1]]
                trivet<-strsplit(st,"")[[1]][strt:(strt+2)]
                st<-sub(paste(trivet,collapse=""),"",st,ignore.case=TRUE)
                splitvet<-strsplit(st,"")[[1]]
                splitvet<-splitvet[splitvet %in% c("A","C","G","T","a","c","g","t")]
                oldbase<-splitvet[1]
                newbase<-splitvet[2]
                trivet[2]<-oldbase
                triplet<-paste(trivet,collapse="")
                mut<-paste(oldbase,newbase,sep=">")
            }else{
                triplet<-st
                mut<-""
            }
            triplets<-c(triplets,triplet)
            mutations<-c(mutations,mut)
        }
    }else{
        triplets<-stvet
        mutations<-stvet
    }
    return(list(triplets,mutations))
}