as-format-methods {GenomicFeatures} | R Documentation

## Coerce to file format structures

### 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 `ID`s 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)

[Package GenomicFeatures version 1.40.1 Index]