findAlternative: Find alternative exons of a gene.
In IVAS: Identification of genetic Variants affecting Alternative Splicing

Description Usage Arguments Value Author(s) References See Also Examples

Search alternative exons among transcript isoforms from a single gene.

1 2	findAlternative(geneid = NULL, txTable = NULL, totalExrange = NULL, totalInrange = NULL, one.chr = NULL)

`geneid`	Ensembl gene name.
`txTable`	The matrix of transcripts including transcript IDs, Ensembl gene names, Ensembl transcript names, transcript start sites, and transcript end sites.
`totalExrange`	A list of GRanges objects including total exon ranges in each transcript resulted from the `exonsBy` function in GenomicFeatures.
`totalInrange`	A list of GRanges objects including total intron ranges in each transcript resulted from the `intronsByTranscript` function in GenomicFeatures.
`one.chr`	The chromosome number that you would like to test

`alterIntron`	A GRanges object with flanking introns of alternative exons
`tableBygene`	An information table of transcripts including transcript IDs, Ensembl gene names, Ensembl transcript names, transcript start sites, and transcript end sites.
`exonRange`	All exons locus of a gene
`intronRange`	All intron locus of a gene

Seonggyun Han, Sangsoo Kim

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Morgan M, and Carey V. Software for Computing and Annotating Genomic Ranges. PLoS Computational Biology, 9, e1003118. 2013.

GRanges, IRanges

    sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
    sample.Txdb <- loadDb(sampleDB)
    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")
    Altvalue <- findAlternative("ENSG00000170889",txTable,trans.exon.range,trans.intron.range,19)