R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Find alternative exons of a gene.

findAlternative

R Documentation

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

Author(s)

Seonggyun Han, Sangsoo Kim

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.

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(IVAS)
Loading required package: GenomicFeatures
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

No methods found in "BiocGenerics" for requests: unlist
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IVAS/findAlternative.Rd_%03d_medium.png", width=480, height=480)
> ### Name: findAlternative
> ### Title: Find alternative exons of a gene.
> ### Aliases: findAlternative
> 
> ### ** 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")
'select()' returned 1:1 mapping between keys and columns
> Altvalue <- findAlternative("ENSG00000170889",txTable,trans.exon.range,trans.intron.range,19)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>