get.annot: Extracts and formats annotations from a .gff file.

In oberstal/pfGO: Plasmodium falciparum functional enrichment analysis tools

Extracts and formats annotations from a .gff file.

Description

Extracts and formats all gene annotations (biotypes "protein_coding_gene", ncRNA_gene", and "pseudogene") from a .gff file. Not required presently for the GO enrichment pipeline, but provides useful context for results. Can be used as-is with a provided gff file as input, or is called by get_pfannot to get the gff file from PlasmoDB.

Usage

get.annot(x)

Arguments

x

input gff file notes on gff format The gff file should be in tabular format with 9 columns, one for each annotated feature associated with a geneID. No formatting is necessary when using the file at the provided url. an annotation created from PlasmoDB's latest P. falciparum .gff file (from PlasmoDB v66; accessed September 28, 2023) pre-formatted using this function is included in this package (pf.annot).

See Also

formatGOdb()

oberstal/pfGO documentation built on April 22, 2024, 7:15 a.m.