as-format-methods: Coerce to file format structures

In GenomicFeatures: Conveniently import and query gene models

Description

These functions coerce a TxDb object to a GRanges object with metadata columns encoding transcript structures according to the model of a standard file format. Currently, BED and GFF models are supported. If a TxDb is passed to export, when targeting a BED or GFF file, this coercion occurs automatically.

Usage

## S4 method for signature 'TxDb'
asBED(x)
## S4 method for signature 'TxDb'
asGFF(x)

Arguments

x	A TxDb object to coerce to a GRanges, structured as BED or GFF.

Value

For asBED, a GRanges, with the columns name, thickStart, thickEnd, blockStarts, blockSizes added. The thick regions correspond to the CDS regions, and the blocks represent the exons. The transcript IDs are stored in the name column. The ranges are the transcript bounds.

For asGFF, a GRanges, with columns type, Name, ID,, and Parent. The gene structures are expressed according to the conventions defined by the GFF3 spec. There are elements of each type of feature: “gene”, “mRNA” “exon” and “cds”. The Name column contains the gene_id for genes, tx_name for transcripts, and exons and cds regions are NA. The ID column uses gene_id and tx_id, with the prefixes “GeneID” and “TxID” to ensure uniqueness across types. The exons and cds regions have NA for ID. The Parent column contains the IDs of the parent features. A feature may have multiple parents (the column is a CharacterList). Each exon belongs to one or more mRNAs, and mRNAs belong to a gene.

Author(s)

Michael Lawrence

Examples

  txdb_file <- system.file("extdata", "hg19_knownGene_sample.sqlite",
                           package="GenomicFeatures")
  txdb <- loadDb(txdb_file)

  asBED(txdb)
  asGFF(txdb)

GenomicFeatures documentation built on April 2, 2021, 6 p.m.