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Parse FLAMES' GFF output

Source: R/find_isoform.R
get_GRangesList.Rd

Parse FLAMES' GFF ouputs into a Genomic Ranges List

Usage

get_GRangesList(
  file,
  feature.type = c("exon", "utr"),
  drop.cols = c("type", "exon_number", "exon_id", "level", "Parent")
)

Arguments

file

the GFF file to parse

feature.type

The type of features to extract from the GFF file. Default is c("exon", "utr").

drop.cols

Columns to drop from the metadata. Default is c("type", "exon_number", "exon_id", "level"), which are exon-specific metadata that may not be relevant when keeping just the first row (exon).

Value

A list containing a GRangesList of isoforms and a DataFrame, which have the same number of rows as the number of unique transcript IDs in the GFF file.