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

In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

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, [e-mail]

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 April 6, 2024, 1:35 p.m.