list.genomes: List genomes created with ORFik

In JokingHero/ORFik: Open Reading Frames in Genomics

List genomes created with ORFik

Description

Given the reference.folder, list all valid references. An ORFik genome is defined as a folder with a file called output.rds that is a named R vector with names gtf and genome, where the values are character paths to those files inside that folder. This makes sure that this reference was made by ORFik and not some other program.

Usage

list.genomes(reference.folder = ORFik::config()["ref"])

Arguments

reference.folder

character path, default: ORFik::config()["ref"].

Value

a data.table with 5 columns:
- character (name of folder)
- logical (does it have a gtf)
- logical (does it have a fasta genome)
- logical (does it have a STAR index)
- logical (only displayed if some are TRUE, does it have protein structure predictions of ORFs from alphafold etc, in folder called 'protein_structure_predictions')
- logical (only displayed if some are TRUE, does it have gene symbol fst file from bioMart etc, in file called 'gene_symbol_tx_table.fst')

Examples

## Run with default config path
#list.genomes()
## Run with custom config path
list.genomes(tempdir())
## Get the path to fasta genome of first organism in list
#readRDS(file.path(config()["ref"], list.genomes()$name, "outputs.rds")[1])["genome"]

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.