etrid2grl: From a transcript identifier to 'GRanges' object

In ComputationalProteomicsUnit/Pbase: Manipulating and exploring protein and proteomics data

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

etrid	A vector of Ensembl transcript identifiers.
ens	A instance of class Mart from biomaRt. If missing, useMart("ensembl", "hsapiens_gene_ensembl") is used.
use.names	If set to TRUE and etrid has names, then the latter are used to name the output.

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)))

ComputationalProteomicsUnit/Pbase documentation built on Aug. 10, 2019, 1:25 a.m.