term_enrichment: Testing for Enrichment and Depletion of Ontology Terms in a...

View source: R/ontology_analysis.R

term_enrichmentR Documentation

Testing for Enrichment and Depletion of Ontology Terms in a Geneset

Description

term_2_gene_count tests for enrichment or depletion of ontology term as compared to randomly sample a set of genes in the reference set of length(your_favourite_experimental_set).

Usage

term_enrichment(parameters_list_exp, parameters_list_ref, stage, modus = "GO",
  twosidetest = "midpval", multCorrect = "bonferroni")

Arguments

parameters_list_exp

the list that is created by term_2_gene_count() for your gene set of interest e.g. down-regulated genes

parameters_list_ref

the list that is created by term_2_gene_count() for your reference gene set.

stage

specify name of experiment.

modus

"GO", "KEGG" or "PANTHER" analysis. Defaults to "GO".

twosidetest

"midpval" or "simpledouble" according to PMID: 17182697. Default is "midpval".

multCorrect

"holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none". Default is "bonferroni".

Details

Please be careful when you set the background or reference set. The background has to be set in a reasonable fashion to get an appropriate answer to a predefined biological question.

Value

term_enrichment creates a dataframe with information of the statistical analysis.
The column named "k" represents the number of genes in the experimental set with an annotation to the row ID.
The column named "m" represents the number of genes in the reference set with an annotation to the row ID.
The columns "kcorrected", "whichmin", "pvl_R" and "pval_L" are essential for the twosided test. Please see PMID: 17182697 and source code.
The column "k_to_n" ratio gives the proportion of genes in the experimental set that have an annotation to the ID specified in the row.
The column "twosided.logpval" is the negative log10 of the twosided pvalue.
"E" stands for enriched and "D" for depleted.


zellerino/BOAT---biological-ontology-analysis-tool documentation built on Jan. 27, 2023, 3:38 p.m.