test_go: Gene Ontology enrichment via topGO

In surh/HMVAR: Human Microbiome Variant Analysis in R

Description

Performs Gene Ontology (GO) enrichment analysis via topGO

Usage

test_go(
  genes,
  annots,
  ontology,
  description,
  algorithm,
  statistic,
  node_size,
  ...
)

## S3 method for class 'character'
test_go(
  genes,
  annots,
  ontology = "BP",
  description = "",
  algorithm = "classic",
  statistic = "fisher",
  node_size = 3,
  ...
)

## S3 method for class 'numeric'
test_go(
  genes,
  annots,
  ontology = "BP",
  description = "",
  algorithm = "classic",
  statistic = "fisher",
  node_size = 3,
  score_threshold = 0.05,
  ...
)

Arguments

genes	Either a character vector with the gene identifiers that are 'significant' or a named numeric vector where the vector names are the gene_identifiers of the universe of genes and the numeric values the genes' scores.
annots	Either a data.frame or tibble that has 'gene_id' and 'terms' column or the result of running annots_to_geneGO on such table.
ontology	Which ontology to test. See help at topGOdata-class.
description	Description for the test. See help at topGOdata-class.
algorithm	Algortithm for test. See help at runTest.
statistic	Statistic to test. See help at runTest.
node_size	Minimum number of genes per term to test that term. See help at topGOdata-class
...	Other arguments to specific methods
score_threshold	If genes is a numeric vector, then this should be the 'significance' threshold. E.g. if scores are p-values a common threshold would be 0.05.

Value

A list with elements topgo_data and topgo_res of class topGOdata and topGOresult respecitveley. If the topGOdata object cannot be created, it will return a list with two NULL entries. If the topGOdata can be created but the test cannot be performed. The topgo_data will contain the topGOdata object and the topgo_res element will be NULL. It will issue warnings anytime that the topgo_res element is NULL

surh/HMVAR documentation built on Aug. 18, 2021, 1:21 a.m.