get_pairs_from_gff

This function creates a features pair file from a GFF file

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

get_pairs_from_gff function

<dl><dt>inFile</dt>
<dd>Path to the input GFF file</dd>
<dt>outFile</dt>
<dd>Path to the output features pair file, if not provided the output will be inFile.pairs</dd>
<dt>fileType</dt>
<dd>Version of the input file (GTF/GFF3). Default AUTO: determined from the file name.</dd>
<dt>forceOverwrite</dt>
<dd>If output file exists, overwrite the existing file. (default FALSE)</dd></dl>

Arguments

Creates a features pair file from a GFF file — get_pairs_from_gff

<dl>

<dt>inFile</dt>
<dd>Path to the input GFF file</dd>


<dt>outFile</dt>
<dd>Path to the output features pair file, if not provided the output will be inFile.pairs</dd>


<dt>fileType</dt>
<dd>Version of the input file (GTF/GFF3). Default AUTO: determined from the file name.</dd>


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

</dl>

get_pairs_from_gff: Creates a features pair file from a GFF file

Description

Usage

Value

Arguments