filter_ontology {mulea}

Filter Ontology

Description

Filtering ontology to contain entries having number of elements (genes or proteins) between a given range. The reason for this is enrichment analysis results can sometimes be skewed by overly specific or broad entries. Filtering ontologies allows you to customize the size of ontology entries, ensuring your analysis aligns with your desired scope.

Usage

filter_ontology(gmt, min_nr_of_elements = NULL, max_nr_of_elements = NULL)

Arguments

gmt

A data.frame which contains the entries (gene or protein sets), imported from a GMT file with the read_gmt function.

min_nr_of_elements

Minimum number of elements. Ontology entries containing as many or fewer elements (genes or proteins) will be excluded.

max_nr_of_elements

Maximum number of elements. Ontology entries containing as many or more elements (genes or proteins) will be excluded.

Value

Return a data.framewhich contains the entries (gene or protein sets) in a similar format that produced by the read_gmt function.

Examples

library(mulea)

# loading and filtering the example ontology from a GMT file
tf_gmt <- read_gmt(file = system.file(
    package="mulea", "extdata", 
    "Transcription_factor_RegulonDB_Escherichia_coli_GeneSymbol.gmt"))
tf_gmt_filtered <- filter_ontology(gmt = tf_gmt,
        min_nr_of_elements = 3,
        max_nr_of_elements = 400)