Title:	R Utilities for GFF Files
Version:	0.1.7
Author:	Juan Antonio Garcia-Martin [cre, aut], Juan Carlos Oliveros [aut, ctb], Rafael Torres-Perez [aut, ctb]
Maintainer:	Juan Antonio Garcia-Martin <ja.garcia@cnb.csic.es>
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.
License:	GPL (≥ 3)
Encoding:	UTF-8
RoxygenNote:	7.1.2
Imports:	withr (≥ 2.4.3), rlang (≥ 0.4.12), stringi (≥ 1.7.6), data.tree (≥ 1.0.0), tibble (≥ 3.1.6), dplyr (≥ 1.0.7), jsonlite (≥ 1.7.2), magrittr (≥ 2.0.1)
Suggests:	DiagrammeR (≥ 1.0.6.1), DiagrammeRsvg (≥ 0.1), rsvg (≥ 2.2.0), rmarkdown (≥ 2.11), knitr (≥ 1.36), GenomicRanges (≥ 1.46.1), rtracklayer (≥ 1.54.0), S4Vectors (≥ 0.32.3)
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2025-05-09 07:32:03 UTC; tono
Repository:	CRAN
Date/Publication:	2025-05-09 09:00:02 UTC

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

Value

The result of calling rhs(lhs).

Test consistency and order of a GFF file

Description

This function tests the consistency and order of a GFF file.

Usage

check_gff(inFile, fileType = c("AUTO", "GFF3", "GTF"))

Arguments

Details

The following list indicates the code and description of the issues detected in GFF3 files

NCOLUMNS_EXCEEDED

Input file contains lines with more than 9 fields

NCOLUMNS_INFERIOR

Input file contains lines with less than 9 fields

TOO_MANY_FEATURE_TYPES

Input file contains too many (more than 100) different feature types

NO_IDs

ID attribute not found in any feature

DUPLICATED_IDs

There are duplicated IDs

ID_IN_MULTIPLE_CHR

The same ID has been found in more than one chromosome

NO_PARENTs

Parent attribute not found in any feature

MISSING_PARENT_IDs

There are missing Parent IDs

PARENT_IN DIFFERENT CHR

There are features whose Parent is located in a different chromosome

PARENT_DEFINED_BEFORE_ID

Feature ids referenced in Parent attribute before being defined as ID

NOT_GROUPED_BY_CHR

Features are not grouped by chromosome

NOT_SORTED_BY_COORDINATE

Features are not sorted by start coordinate

NOT_VALID_WARNING

File cannot be recognized as valid GFF3. Parsing warnings.

NOT_VALID_ERROR

File cannot be recognized as valid GFF3. Parsing errors.

The following list indicates the code and description of the issues detected in GTF files

NCOLUMNS_EXCEEDED

Input file contains lines with more than 9 fields

NCOLUMNS_INFERIOR

Input file contains lines with less than 9 fields

TOO_MANY_FEATURE_TYPES

Input file contains too many (more than 100) different feature types

NO_GENE_ID_ATTRIBUTE

gene_id attribute not found in any feature

MISSING_GENE_IDs

There are features without gene_id attribute

NO_GENE_FEATURES

Gene features are not included in this GTF file

DUPLICATED_GENE_IDs

There are duplicated gene_ids

GENE_ID_IN_MULTIPLE_CHR

The same gene_id has been found in more than one chromosome

NO_TRANSCRIPT_ID_ATTRIBUTE

transcript_id attribute not found in any feature There are no elements with transcript_id attribute

MISSING_TRANSCRIPT_IDs

There are features without transcript_id attribute

NO_TRANSCRIPT_FEATURES

Transcript features are not included in this GTF file

DUPLICATED_TRANSCRIPT_IDs

There are duplicated transcript_ids

TRANSCRIPT_ID_IN_MULTIPLE_CHR

The same transcript_id has been found in more than one chromosome

DUPLICATED_GENE_AND_TRANSCRIPT_IDs

Same id has been defined as gene_id and transcript_id

NOT_GROUPED_BY_CHR

Features are not grouped by chromosome

NOT_SORTED_BY_COORDINATE

Features are not sorted by start coordinate

NOT_VALID_WARNING

File cannot be recognized as valid GTF. Parsing warnings.

NOT_VALID_ERROR

File cannot be recognized as valid GTF. Parsing errors.

Value

A data frame of detected issues, including a short code name, a description and estimated severity each. In no issues are detected the function will return an empty data frame.

Examples

test_gff3<-system.file("extdata", "eden.gff3", package="Rgff")
check_gff(test_gff3)

Test consistency and order of a GFF3 file

Description

This function test consistency and order of a GFF3 file.

Usage

check_gff3(gffFile)

Arguments

Value

A data frame with the errors detected

Test consistency and order of a GTF file

Description

This function tests consistency and order of a GTF file. Optionally, can fix some of the consistency errors and sort the GTF file.

Usage

check_gtf(gtfFile)

Arguments

Value

A data frame with the errors detected

Analyses the feature type hierarchy of a GFF file

Description

Based on the feature type hierarchy a GFF file, this function creates and returns a feature tree or a feature dependency table.

Usage

get_features(
  inFile,
  includeCounts = FALSE,
  outFormat = c("tree", "data.frame", "JSON"),
  fileType = c("AUTO", "GFF3", "GTF")
)

Arguments

Value

Depending on the outFormat selected returns a feature tree (tree), a feature dependency table as data.frame (data.frame) or a feature dependency table as JSON object (JSON)

Examples

test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
get_features(test_gff3)

Creates a features pair file from a GFF file

Description

This function creates a features pair file from a GFF file

Usage

get_pairs_from_gff(
  inFile,
  outFile,
  fileType = c("AUTO", "GFF3", "GTF"),
  forceOverwrite = FALSE
)

Arguments

Value

Path to the generated features pair file

Creates a features pair file from a GFF file

Description

This function creates a features pair file from a GFF file

Usage

get_pairs_from_gff3(gffFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the generated features pair file

Creates a features pair file from a GTF file

Description

This function creates a features pair file from a GTF file

Usage

get_pairs_from_gtf(gtfFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the generated features pair file

Creates a features path file from a GFF file

Description

This function creates a features path file from a GFF file

Usage

gff3_to_paths(gffFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the generated features path file

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

Description

This function summarizes the number of features of each type in a GFF file and returns the statistics

Usage

gff_stats(inFile)

Arguments

Value

A tibble with the summary data

Examples

test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
gff_stats(test_gff3)

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

Description

This function summarizes the number of features of each type in each chromosome of a GFF file and returns the statistics

Usage

gff_stats_by_chr(inFile)

Arguments

Value

A tibble with the summary data

Examples

test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
gff_stats_by_chr(test_gff3)

Converts a GTF file into a GFF3 file

Description

This function converts a GTF file into a GFF3 file mantaining the feature hierarchy defined by the gene_id and transcript_id attributes. The remaining attributes of each feature will be kept with the same name and value.

Usage

gtf_to_gff3(gtfFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the generated GFF3 file

Examples

## Not run: 
test_gtf<-system.file("extdata", "AthSmall.gtf", package="Rgff")
gtf_to_gff3(test_gtf)

## End(Not run)

Creates a features path file from a GTF file

Description

This function creates a features path file from a GTF file

Usage

gtf_to_paths(gtfFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the generated features path file

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

Description

This function plots the feature tree from a GFF file or, if an output file name is provided, exports an image of in the desired format ("png", "pdf" or "svg"). Packages "DiagrammeR", "DiagrammeRsvg" and "rsvg" must be installed to use this function.

Usage

plot_features(
  inFile,
  outFile,
  includeCounts = FALSE,
  fileType = c("AUTO", "GFF3", "GTF"),
  exportFormat = c("png", "pdf", "svg")
)

Arguments

Value

Path of the output features image file

Examples

if(requireNamespace("DiagrammeR")){
    test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
    plot_features(test_gff3)
}

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

Description

This function creates a SAF file from a GTF/GFF3 features for the given blocks and features

Usage

saf_from_gff(
  inFile,
  outFile,
  fileType = c("AUTO", "GFF3", "GTF"),
  forceOverwrite = FALSE,
  features = c("gene > exon"),
  sep = ">"
)

Arguments

Value

Path to the generated SAF file

Examples

test_gff3<-system.file("extdata", "AthSmall.gff3", package="Rgff")
## Default usage, extract gene features by exon blocks 
saf_from_gff(test_gff3)
## Define only feature without block to count reads within the whole genomic locus 
saf_from_gff(test_gff3, features=c("gene"))
## Define multiple features for counting readsoverlapping only in exonic regions 
saf_from_gff(test_gff3, features=c("gene > exon", "ncRNA_gene > exon"))

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

Description

This function creates a SAF file from a GFF3 for the given blocks and features

Usage

saf_from_gff3(
  gffFile,
  outFile,
  forceOverwrite = FALSE,
  features = c("gene > exon"),
  sep = ">"
)

Arguments

Value

Path to the generated SAF file

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

Description

This function creates a SAF file from a features path file for the given blocks and features

Usage

saf_from_paths(
  pathsFile,
  groupBy = c("mRNA", "gene"),
  block = c("exon", "CDS")
)

Arguments

Value

SAF formatted data frame for the given blocks and features

Sorts a GTF/GFF3 file

Description

This function produces a sorted GFF file from an unsorted GFF file. The default order is by Chromosome, Start, End (reverse) and feature (based on the precedency in feature tree)

Usage

sort_gff(
  inFile,
  outFile,
  fileType = c("AUTO", "GFF3", "GTF"),
  forceOverwrite = FALSE
)

Arguments

Value

Path to the sorted feature file

Examples

test_gff3<-system.file("extdata", "eden.gff3", package="Rgff")
sort_gff(test_gff3)

Sorts a GFF3 file

Description

This function produces a sorted GFF3 file from an unsorted GFF3 file. The output file will be sorted by Chromosome, Start, End (reverse) and feature (based on the precedency in feature tree)

Usage

sort_gff3(gffFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the sorted GFF3 file

Sorts a GTF file

Description

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

Usage

sort_gtf(gtfFile, outFile, forceOverwrite = FALSE)

Arguments

Value

Path to the sorted GTF file