filterGtf: Filter gtf file by target chromosomes
In HatsuneCode/TrustVDJ: Tools for Immune Repertoire Analysis

filterGtf

R Documentation

Filter gtf file by target chromosomes

Description

filterGtf reads gtf file and filter it by target chromosomes. (.gz supported)

Usage

filterGtf(gtf, chromosomes = NULL, out = NULL, sep = "\t", verbose = TRUE)

Arguments

`gtf`	character. Path to gtf file.
`chromosomes`	character. Target chromosomes.
`out`	character. Output file.
`sep`	character. Each gtf line separator. Default `'\t'`
`verbose`	logical. Print progress. Default TRUE

Value

if success, return TRUE

Examples

gtf = system.file('extdata', 'IMGT_Homo_sapiens.gtf.gz', package = 'TrustVDJ')
filterGtf(gtf, c('IGHD1-1*01', 'TRDD1*01'), 'filter.gtf')
gtf = readLines('filter.gtf')
file.remove('filter.gtf')
cat(paste(gtf, '\n', collapse = ''))

HatsuneCode/TrustVDJ documentation built on Aug. 13, 2022, 9:36 p.m.