load_annotation: Get a set of filtered cds from an imported GTF GRanges

load_annotationR Documentation

Get a set of filtered cds from an imported GTF GRanges

Description

Get a set of filtered cds from an imported GTF GRanges

Usage

load_annotation(
  gtf,
  fafile,
  add_uorfs = TRUE,
  ignore_orf_validity = FALSE,
  keep_cols = c("gene_id", "transcript_id", "gene_name", "type"),
  DEFAULT_CIRC_SEQS = NULL,
  findUORFs_args = c(minimumLength = 0)
)

Arguments

gtf

A GTF with gene annotation

fafile

FaFile; path to a genomic Fasta file

add_uorfs

Whether to look for and include uORFs

ignore_orf_validity

Boolean; flag whether to include ORFs missing a valid stop codon

keep_cols

columns to save from the gtf metadata

DEFAULT_CIRC_SEQS

default chromsoomes to treat as circular

findUORFs_args

Additional arguments to pass to ORFik::findUORFs

Details

This takes only coding sequences which are a multiple of 3bp and have a start and a stop on either end. it always returns coding sequences without the stops, regardless of their extent in the input.

Value

a list containing annotation objects used by other functions.

Author(s)

Dermot Harnett, dermot.p.harnett@gmail.com

Examples

gtf <- system.file("extdata", "gcv37.anno.chr22.gtf",
  package = "Ribostan",
  mustWork = TRUE
)
fafile <- system.file("extdata", "chr22.fa.gz",
  package = "Ribostan",
  mustWork = TRUE
)
file.copy(fafile, ".")
system2("gunzip -f chr22.fa.gz")
fafile <- "chr22.fa"
anno <- load_annotation(gtf, fafile)

zslastman/RiboStan documentation built on June 12, 2024, 1:59 a.m.