Rgff (version 0.1.6)

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

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 = ">"
)

Value

Path to the generated SAF file

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 '>')