get_ribofasta_anno: This creates a minimal annotation object from a gencode style...
In zslastman/RiboStan: Estimates Isoform Specific RPF Footprint Densities

get_ribofasta_anno

R Documentation

This creates a minimal annotation object from a gencode style fasta

Description

This creates a minimal annotation object from a gencode style fasta

Usage

get_ribofasta_anno(ribofasta)

Arguments

ribofasta

A gencode style fasta to which RPFs were aligned

Details

The Ribosome densities are saved in salmon format

Value

An annotation object with cdsstarts/stops

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"
ext_fasta <- make_ext_fasta(gtf, fafile, outfasta = "tmp.fa", fpext = 50, tpext = 50)
get_ribofasta_anno(ext_fasta)

zslastman/RiboStan documentation built on April 6, 2024, 1:35 p.m.