getFeatures: Parses a genome file in GFF format into a list of...

In kewiechecki/peakToGene: Functions to assign regulatory elements to genomic features.

Parses a genome file in GFF format into a list of GRangesLists organized by gene and genomic feature.

Description

Parses a genome file in GFF format into a list of GRangesLists organized by gene and genomic feature.

Usage

getFeatures(
  gff,
  prefix = "KY2019:",
  tssflank = c(1107, 107),
  tsswindow = 10000,
  ttswindow = 10000,
  ...
)

Arguments

gff	Path to a genome file in GFF format.
prefix	Prefix to append to gene IDs.
tssflank	Numeric vector of length 2 giving the window in bp upstream and downstream of the TSS to use as the promoter.
tsswindow	How many bp upstream of the promoter to consider as upstream of a gene.
ttswindow	How many bp downstream of the TTS to consider as downstream of a gene.

See Also

mergeMotifs, motifmatchr::matchMotifs

kewiechecki/peakToGene documentation built on June 8, 2025, 5:18 a.m.