extract_field_from_gencode: Extract field from gencode GTF file

In jokergoo/epik: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Extract field from gencode GTF file

Usage

extract_field_from_gencode(file, level = "gene",
    primary_key = "gene_id", field = "gene_name")

Arguments

file	the input GTF file
level	level of the annotation (e.g. gene, transcript, exon, the third column in GTF file)
primary_key	primary field
field	field to be retrieved

Details

Although GTF file can be imported by e.g. makeTxDbFromGFF, some information in the original GTF file will not be imported. This function aims to extract additionally information from GTF file.

The function calls external Perl script, so you need to have Perl installed.

Value

A vector in which 'primary_key' corresponds to the name and 'field' corresponds to the value.

Author(s)

Zuguang Gu <[e-mail]>

See Also

available_gencode_fields lists all possible values for primary_key and field.

Examples

## Not run: 
download.file("ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_19/gencode.v19.annotation.gtf.gz",
    destfile = "gencode.v19.annotation.gtf.gz")
extract_field_from_gencode("gencode.v19.annotation.gtf.gz")
extract_field_from_gencode("gencode.v19.annotation.gtf.gz", field = "gene_type")

## End(Not run)
NULL

jokergoo/epik documentation built on Sept. 28, 2019, 9:20 a.m.