R/findAlternative.R

In IVAS: Identification of genetic Variants affecting Alternative Splicing

findAlternative <- function(geneid=NULL,txTable=NULL,totalExrange=NULL,totalInrange=NULL,one.chr=NULL){
    tableBygene <- txTable[which(txTable[,"GENEID"]==geneid),]
    txid <- tableBygene[,"TXID"]
    txstarts <- tableBygene[,"TXSTART"]
    txends <- tableBygene[,"TXEND"]
    each.exon <- totalExrange[as.character(txid)]
    each.intron <- totalInrange[as.character(txid)]
    if (length(txid) > 1 & length(start(unlist(each.intron))) > 0){
        nosigintron <- NULL
        strandinfo <- paste(strand(each.exon)[[1]][1],"",sep="")
        st.intron <- unlist(start(each.intron))
        en.intron <- unlist(end(each.intron))
        sortintron <- paste(st.intron,en.intron,sep="-")
        intronName <- unique(sortintron)
        for (i in 1:length(intronName)){
            spl.cal <- as.integer(strsplit(intronName[i],"-")[[1]])
            startcount <- length(txid) - length(txstarts[(spl.cal[1] < txstarts & spl.cal[2] < txstarts) | (spl.cal[1] > txends & spl.cal[2] > txends)])
            if (table(sortintron)[intronName[i]] == startcount){
                nosigintron <- append(nosigintron,intronName[i])
            }
        }
        intronName <- intronName[!is.element(intronName,nosigintron)]
        intronrange <- unlist(strsplit(intronName,"-"))
        if (length(intronrange) > 0){
            In.table <- matrix(intronrange,ncol=2,byrow=TRUE)
            colnames(In.table) <- c("start","end")
            not.sig <- nrow(In.table)+1
            for (z in 1:nrow(In.table)){
                match.num <- NULL
                match.num <- which(st.intron==In.table[z,1] & en.intron==In.table[z,2])
                one.num <- NULL
                last.num <- NULL
                cal.re <- NULL
                cal.re2 <- NULL
                if (is.element(1,match.num) | is.element(length(st.intron),match.num)){
                    one.num <- which(match.num==1)
                    last.num <- which(match.num==length(st.intron))
                }
                else {
                    if (length(which(names(st.intron[match.num]) != names(st.intron[match.num-1]))) != 0){
                        one.num <- match.num[which(names(st.intron[match.num]) != names(st.intron[match.num-1]))]
                    }
                    else if(length(which(names(st.intron[match.num]) != names(st.intron[match.num+1]))) != 0){
                        last.num <- match.num[which(names(st.intron[match.num]) != names(st.intron[match.num+1]))]
                    }
                }
                if (length(one.num) > 0){
                    for (y in 1:length(one.num)){
                        ex.start <- tableBygene[tableBygene[,1]==names(one.num[y]),"TXSTART"]
                        cal.re <- which(ex.start > st.intron & ex.start < en.intron)
                    }
                }
                else if (length(last.num) > 0){
                    for (y in 1:length(last.num)){
                        ex.end <- tableBygene[tableBygene[,1]==names(last.num[y]),"TXEND"]
                        cal.re2 <- which(ex.end > st.intron & ex.end < en.intron)
                    }
                }
                if (length(match.num) == 1 & (length(cal.re) + length(cal.re2) > 0)){
                    not.sig <- c(not.sig,z)
                }
            }
            if (length(In.table[-not.sig,1]) > 0){
                In.table <- In.table[-not.sig,]
                In.table <- matrix(In.table,ncol=2)
                colnames(In.table) <- c("start","end")
                irange <- IRanges(start=as.integer(In.table[,"start"]),end=as.integer(In.table[,"end"]))
                alterIntron <- GRanges(seqnames=Rle(one.chr),ranges=irange,strand=strandinfo)
                return.value <- list(alterIntron,tableBygene,each.exon,each.intron)
                names(return.value) <- c("alterIntron","tableBygene","exonRange","intronRange")
                return (return.value)
            }
        }
    }
    return (NULL)
}