overrep_test: overrep_test

In laurabiggins/GOcategoryStats: Provides statistics for Gene Ontology categories (Title Case)

Description

Overrepresentation test - Functional (usually gene ontology) analysis

Usage

overrep_test(categories, query_genes, bg_genes, min_query = 3,
  pval_threshold = 0.05, ease = TRUE, sig_digits = 4,
  mult_test = TRUE, super_strict = FALSE)

Arguments

categories	list of named character vectors containing the functional groups. Each vector should contain gene names or IDs. The name of each vector should be the functional category.
query_genes	character vector of gene names
bg_genes	character vector of gene names to use as the background set containing genes and associated information including location of genes
min_query	minimum number of query genes in the category for it be tested, no point having a category with one query gene in it
pval_threshold	p value threshold. Only results with p-value/corrected p-value less than this thrreshold will be returned.
mult_test	apply multiple testing correction (Benjamini-Hochberg FDR is used) and use the corrected value to filter for significant results. This should usually be set to TRUE (default). If set to false, the correction is still applied but the uncorrected pvalue is used to filter by.
super_strict	stricter pvalue correction where it takes the number of tests as being the total number of functional categories. By default the number of tests corrected for is only the number of functional categories that contain min_query genes

Value

results of functional overrepresentation test. If no categories have a p-value <= pval_threshold a NULL object will be returned.

Examples

go_results <- overrep_test(all_go_categories, genes_1, bg_genes)
head(go_results)

laurabiggins/GOcategoryStats documentation built on Oct. 27, 2019, 11:36 a.m.