findOversnp: Find SNPs which belong to alternative exons and flanking...

In IVAS: Identification of genetic Variants affecting Alternative Splicing

Description

Find SNPs which belong to alternative exons and flanking introns of them.

Usage

    findOversnp(altInvalue = NULL, snprange = NULL)

Arguments

altInvalue	A list data set from the findAlternative function.
snprange	A matrix of SNP ranges.

Value

This function returns a matrix with SNPs which are located in alternative exons and flanking introns and ranges of those SNPs.

Author(s)

Seonggyun Han, Sangsoo Kim

See Also

findOverlaps

Examples

    sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
    sample.Txdb <- loadDb(sampleDB)
    data(samplesnplocus)
    data(samplesnp)
    filtered.txdb <- chrseparate(sample.Txdb,19)
    trans.exon.range <- exonsBy(filtered.txdb,by="tx")
    trans.intron.range <- intronsByTranscript(filtered.txdb)
    txTable <- select(filtered.txdb, keys=names(trans.exon.range),
                                        columns=c("TXID","TXNAME","GENEID","TXSTART","TXEND"), keytype="TXID")
    ch.snp.locus <- as.matrix(samplesnplocus[samplesnplocus[,2] == 19,])
    ch.snps <- matrix(ch.snp.locus[is.element(ch.snp.locus[,1],rownames(samplesnp)),],ncol=3,byrow=FALSE)
    ch.snps.range <- GRanges(seqnames=Rle(19),ranges=IRanges(start=as.integer(ch.snps[,3]),
                                                                                                                     end=as.integer(ch.snps[,3])),metadata=ch.snps[,1])
    Altvalue <- findAlternative("ENSG00000170889",txTable,trans.exon.range,trans.intron.range,19)
    overlapsnp <- findOversnp(Altvalue,ch.snps.range)

IVAS documentation built on Nov. 8, 2020, 5:52 p.m.