id2name: Map internal ids to external names for a given feature type

In Bioconductor/GenomicFeatures: Conveniently import and query gene models

Map internal ids to external names for a given feature type

Description

Utility function for retrieving the mapping from the internal ids to the external names of a given feature type.

Usage

id2name(txdb, feature.type=c("tx", "exon", "cds"))

Arguments

txdb	A TxDb object.
feature.type	The feature type for which the mapping must be retrieved.

Details

Transcripts, exons and CDS parts in a TxDb object are stored in seperate tables where the primary key is an integer called feature internal id. This id is stored in the "tx_id" column for transcripts, in the "exon_id" column for exons, and in the "cds_id" column for CDS parts. Unlike other commonly used ids like Entrez Gene IDs or Ensembl IDs, this internal id was generated at the time the TxDb object was created and has no meaning outside the scope of this object.

The id2name function can be used to translate this internal id into a more informative id or name called feature external name. This name is stored in the "tx_name" column for transcripts, in the "exon_name" column for exons, and in the "cds_name" column for CDS parts.

Note that, unlike the feature internal id, the feature external name is not guaranteed to be unique or even defined (the column can contain NAs).

Value

A named character vector where the names are the internal ids and the values the external names.

Author(s)

Hervé Pagès

See Also

• transcripts, transcriptsBy, and transcriptsByOverlaps, for how to extract genomic features from a TxDb object.

• The TxDb class.

Examples

txdb1_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                          package="GenomicFeatures")
txdb1 <- loadDb(txdb1_file)
id2name(txdb1, feature.type="tx")[1:4]
id2name(txdb1, feature.type="exon")[1:4]
id2name(txdb1, feature.type="cds")[1:4]

txdb2_file <- system.file("extdata", "Biomart_Ensembl_sample.sqlite",
                          package="GenomicFeatures")
txdb2 <- loadDb(txdb2_file)
id2name(txdb2, feature.type="tx")[1:4]
id2name(txdb2, feature.type="exon")[1:4]
id2name(txdb2, feature.type="cds")[1:4]

Bioconductor/GenomicFeatures documentation built on April 29, 2024, 11:23 a.m.