load_microbesonline_go: Extract the set of GO categories by microbesonline locus

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Extract the set of GO categories by microbesonline locus

Description

The microbesonline is such a fantastic resource, it is a bit of a shame that it is such a pain to query.

Usage

load_microbesonline_go(
  id = NULL,
  species = NULL,
  table_df = NULL,
  id_column = "name",
  data_column = "GO",
  name = NULL
)

Arguments

id	Which species to query.
species	Microbesonline species.
table_df	Pre-existing data frame of annotations containing GO stuff.
id_column	This no longer uses MySQL, so which column from the html table to pull?
data_column	Similar to above, there are lots of places from which one might extract the data.
name	Allowing for non-specific searches by species name.

Details

Tested in test_42ann_microbes.R I am not 100 ontology accessions. At the very least, it does return a large number of them, which is a start.

Value

data frame of GO terms from www.microbesonline.org

See Also

[tidyr]

Examples

 pa14_microbesonline_go <- load_microbesonline_go(species = "PA14")
 head(pa14_microbesonline_go)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.