check_gff {BUSpaRse}R Documentation

Check inputs to tr2g_gtf and tr2g_gff3

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.

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.

Value

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


[Package BUSpaRse version 1.0.0 Index]