R: From a transcript identifier to 'GRanges' object

etrid2grl {Pbase}

R Documentation

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

`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)))

[Package Pbase version 0.20.0 Index]