pf.annot: All _P. falciparum_ gene-product annotations.
In oberstal/pfGO: Plasmodium falciparum functional enrichment analysis tools

pf.annot

R Documentation

All P. falciparum gene-product annotations.

Description

A dataset containing all P. falciparum gene-product annotations taken directly from gff file(reference strain 3D7). Only "gene" entries are kept to remove redundancy.

Usage

data(pf.annot)

Format

A data frame of 5720 rows and 9 columns.

seqid: chromosome ID.
geneStart: gene start coordinate.
geneEnd: gene end coordinate.
strand: gene strand.
type: type of annotation. Here protein-coding genes, ncRNA genes and pseudogenes are kept.
geneID: gene ID.
description: functional annotation.
geneName: the gene symbol, or short name, if one exists; otherwise the geneID is used.
source: annotation source.

Details

Keep in mind:

These data aren't explicitly required for running any enrichments with this package. They are included for reference to aid exploring your enrichment results.

Some redundant columns were filtered/removed from the original data source.

Updated versions can be generated using the get.pfannot function and specifying the url or filepath to your preferred plasmoDB .gff file. Note the run.topGO.meta function currently calls get.pfannot with plasmoDB release 66 to annotate the significant-genes-in-enriched-terms output.