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Rgff (version 0.1.6)

R Utilities for GFF Files

Description

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.

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Version

Install

install.packages('Rgff')

Monthly Downloads

224

Version

0.1.6

License

GPL (>= 3)

Maintainer

Juan Antonio Garcia-Martin

Last Published

September 30th, 2022

Functions in Rgff (0.1.6)

saf_from_gff

Creates a SAF file from a GTF/GFF3 features for the given pairs of blocks and features
sort_gff

Sorts a GTF/GFF3 file
saf_from_paths

Generates SAF formatted data from a features path file for the given blocks and features
saf_from_gff3

Creates a SAF file from a GFF3 for the given pairs of blocks and features, note that groupBy and block vectors must have the same length
get_pairs_from_gff3

Creates a features pair file from a GFF file
gff_stats_by_chr

Summarizes the number of elements of each type in each chromosome of a GFF file
gff_stats

Summarizes the number of features of each type in a GFF file
check_gff

Test consistency and order of a GFF file
get_pairs_from_gff

Creates a features pair file from a GFF file
get_pairs_from_gtf

Creates a features pair file from a GTF file
check_gff3

Test consistency and order of a GFF3 file
gff3_to_paths

Creates a features path file from a GFF file
plot_features

Plots or exports an image of the feature tree from a GFF file
sort_gtf

Sorts a GTF file
%>%

Pipe operator
sort_gff3

Sorts a GFF3 file
gtf_to_gff3

Converts a GTF file into a GFF3 file
get_features

Analyses the feature type hierarchy of a GFF file
check_gtf

Test consistency and order of a GTF file
gtf_to_paths

Creates a features path file from a GTF file