available_gencode_fields: Returns all supported fields in GTF file

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

Description

Returns all supported fields in GTF file

Usage

available_gencode_fields(file, level = "gene")

Arguments

file	the input GTF file
level	level of the annotation (e.g. gene, transcript, exon, the third column in GTF file)

Details

These fields are stored in the 9th column in the GTF file.

Value

A vector of available fields.

Author(s)

Zuguang Gu <[e-mail]>

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")
available_gencode_fields("gencode.v19.annotation.gtf.gz", level = "gene")
available_gencode_fields("gencode.v19.annotation.gtf.gz", level = "transcript")

## End(Not run)
NULL

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