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

In oberstal/pfGO: Plasmodium falciparum functional enrichment analysis tools

Extracts and formats annotations from a gff file from PlasmoDB.

Description

Extracts and formats annotations from a gff file from PlasmoDB. Not required presently for the GO enrichment pipeline, but provides useful context for results. Opens a connection to the .gff file from PlasmoDB without downloading it, then calls get_annot() to extract and format the annotation.

Usage

get.pfannot(
  gff_url =
    "https://plasmodb.org/common/downloads/release-66/Pfalciparum3D7/gff/data/PlasmoDB-66_Pfalciparum3D7.gff"
)

Arguments

gff_url

connection to .gff file. Defaults to https://plasmodb.org/common/downloads/release-66/Pfalciparum3D7/gff/data/PlasmoDB-66_Pfalciparum3D7.gff

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 provided url.

an annotation created from PlasmoDB's P. falciparum gff file (v. 66, accessed September 28, 2023) pre-formatted using this function and ready for run.topGO.meta is included in this package (pf.annot).

You will need to update the gff url accordingly to the latest version when PlasmoDB is updated.

See Also

get.annot()

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