saf_from_gff3: Creates a SAF file from a GFF3 for the given pairs of blocks...

In Rgff: R Utilities for GFF Files

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

gffFile	Path to the input GFF file
outFile	Path to the output SAF file, if not provided the output path will be the input path (without extension) with the suffix ".groupBy1-block1.groupBy2-block2(...).saf"
forceOverwrite	If output file exists, overwrite the existing file. (default FALSE)
features	Vector of pairs of features, separated by '>' (see sep argument), to be used respectively as "group by" and "block"
sep	Separator of each "group by" and "block" provided in the feature argument (default '>')

Value

Path to the generated SAF file

Rgff documentation built on Sept. 30, 2022, 5:08 p.m.