findAlternative {IVAS} | R Documentation |
Search alternative exons among transcript isoforms from a single gene.
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 |
totalInrange |
A list of GRanges objects including total intron ranges in each transcript resulted from the |
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.
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)