goseq_table: Enhance the goseq table of gene ontology information.

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

Enhance the goseq table of gene ontology information.

Description

While goseq has some nice functionality, the table of outputs it provides is somewhat lacking. This attempts to increase that with some extra helpful data like ontology categories, definitions, etc.

Usage

goseq_table(df, file = NULL)

Arguments

df	Dataframe of ontology information. This is intended to be the output from goseq including information like numbers/category, GOids, etc. It requires a column 'category' which contains: GO:000001 and such.
file	Csv file to which to write the table.

Value

Ontology table with annotation information included.

See Also

[goseq] [GO.db]

Examples

## Not run: 
 annotated_go = goseq_table(go_ids)
 head(annotated_go, n = 1)
 ## >        category numDEInCat numInCat over_represented_pvalue
 ## > 571  GO:0006364          9       26            4.655108e-08
 ## >      under_represented_pvalue       qvalue ontology
 ## > 571                 1.0000000 6.731286e-05       BP
 ## >                                term
 ## > 571                 rRNA processing
 ## >                               synonym
 ## > 571        "35S primary transcript processing, GO:0006365"
 ## >        secondary    definition
 ## > 571    GO:0006365   Any process involved in the conversion of a primary ribosomal
 ##          RNA (rRNA) transcript into one or more mature rRNA molecules.

## End(Not run)

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