check_gff: Check inputs to tr2g_gtf and tr2g_gff3

In BUSpaRse: kallisto | bustools R utilities

Description

This function validates inputs to tr2g_gtf and tr2g_gff3 and throws error early if some inputs are wrong.

Usage

check_gff(format, file, transcript_id, gene_id)

Arguments

format	Whether it's gtf or gff3.
file	Path to a GTF file to be read. The file can remain gzipped. Use getGTF from the biomartr package to download GTF files from Ensembl, and use getGFF from biomartr to download GFF3 files from Ensembl and RefSeq.
transcript_id	Character vector of length 1. Tag in attribute field corresponding to transcript IDs. This argument must be supplied and cannot be NA or NULL. Will throw error if tag indicated in this argument does not exist.
gene_id	Character vector of length 1. Tag in attribute field corresponding to gene IDs. This argument must be supplied and cannot be NA or NULL. Note that this is different from gene symbols, which do not have to be unique. This can be Ensembl or Entrez IDs. However, if the gene symbols are in fact unique for each gene, you may supply the tag for human readable gene symbols to this argument. Will throw error if tag indicated in this argument does not exist. This is typically "gene_id" for annotations from Ensembl and "gene" for refseq.

Value

Nothing, will throw error if there's a problem.

BUSpaRse documentation built on March 3, 2021, 2:01 a.m.