IVAS (version 1.4.0)

findAlternative: Find alternative exons of a gene.

Description

Search alternative exons among transcript isoforms from a single gene.

Usage

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

Arguments

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 GRnages objects inclucing total exon ranges in each transcript resulted from the exonsBy function in GenomicFeatures.

totalInrange

A list of GRnages objects inclucing total intron ranges in each transcript resulted from the intronsByTranscript function in GenomicFeatures.

one.chr

The chromosome number that you want.

Value

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

References

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.

See Also

GRanges, IRanges

Examples

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)