From a transcript identifier to GRanges object

Description

This function takes on or more Ensembl transcript identifiers, queries Biomart and constructs a GRangesList object as would Gviz::BiomartGeneRegionTrack for a genomic region (in fact, currently most of the code has been taken from Gviz::.fetchBMData and GViz::.chrName is used to validate chromosome names).

Usage

etrid2grl(etrid, ens, use.names = FALSE)

Arguments

Value

A GRangesList object of length length(etrid).

Author(s)

Laurent Gatto

Examples

id <- c("ENST00000612959", "ENST00000317091")
grl1 <- etrid2grl(id[1])
grl1
grl <- etrid2grl(id)
stopifnot(all.equal(id, names(grl)))

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.
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Type 'license()' or 'licence()' for distribution details.

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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(Pbase)
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: Rcpp
Loading required package: Gviz
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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid

This is Pbase version 0.12.2

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Pbase/etrid2grl.Rd_%03d_medium.png", width=480, height=480)
> ### Name: etrid2grl
> ### Title: From a transcript identifier to 'GRanges' object
> ### Aliases: etrid2grl
> 
> ### ** Examples
> 
> id <- c("ENST00000612959", "ENST00000317091")
> grl1 <- etrid2grl(id[1])
> grl1
GRangesList object of length 1:
$ENST00000612959 
GRanges object with 8 ranges and 7 metadata columns:
      seqnames               ranges strand |        feature            gene
         <Rle>            <IRanges>  <Rle> |    <character>     <character>
  [1]    chr17 [30116807, 30116863]      + |           utr5 ENSG00000126653
  [2]    chr17 [30172542, 30172589]      + |           utr5 ENSG00000126653
  [3]    chr17 [30172590, 30172598]      + | protein_coding ENSG00000126653
  [4]    chr17 [30178071, 30178199]      + | protein_coding ENSG00000126653
  [5]    chr17 [30179090, 30179297]      + | protein_coding ENSG00000126653
  [6]    chr17 [30180908, 30181016]      + | protein_coding ENSG00000126653
  [7]    chr17 [30184615, 30185674]      + | protein_coding ENSG00000126653
  [8]    chr17 [30185675, 30186474]      + |           utr3 ENSG00000126653
                 exon      transcript      symbol      rank     phase
          <character>     <character> <character> <numeric> <integer>
  [1] ENSE00003738663 ENST00000612959       NSRP1         1        -1
  [2] ENSE00003689679 ENST00000612959       NSRP1         2        -1
  [3] ENSE00003689679 ENST00000612959       NSRP1         2        -1
  [4] ENSE00003519306 ENST00000612959       NSRP1         3         0
  [5] ENSE00003659893 ENST00000612959       NSRP1         4         0
  [6] ENSE00003562538 ENST00000612959       NSRP1         5         1
  [7] ENSE00003744594 ENST00000612959       NSRP1         6         0
  [8] ENSE00003744594 ENST00000612959       NSRP1         6        -1

-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
> grl <- etrid2grl(id)
> stopifnot(all.equal(id, names(grl)))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>