sort_gtf

This function produces a sorted GTF file from an unsorted GTF file.
The default order is by Chromosome, Start, End (reverse) and feature (gene -&gt; transcript -&gt; OTHERS)

internal

R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.

Juan Antonio Garcia-Martin

Rgff

R Utilities for GFF Files

Juan Carlos Oliveros

Rafael Torres-Perez

sort_gtf function

<dl><dt>gtfFile</dt>
<dd>Path to the input GTF file</dd>
<dt>outFile</dt>
<dd>Path to the output GTF file, if not provided the output will be the input path (without extension) with the suffix sorted.gtf</dd>
<dt>forceOverwrite</dt>
<dd>If output file exists, overwrite the existing file. (default FALSE)</dd></dl>

Arguments

Sorts a GTF file — sort_gtf

<dl>

<dt>gtfFile</dt>
<dd>Path to the input GTF file</dd>


<dt>outFile</dt>
<dd>Path to the output GTF file, if not provided the output will be the input path (without extension) with the suffix sorted.gtf</dd>


<dt>forceOverwrite</dt>
<dd>If output file exists, overwrite the existing file. (default FALSE)</dd>

</dl>

sort_gtf: Sorts a GTF file

Description

Usage

Value

Arguments