CLfeats: produce a data.frame of features relevant to a Cell Ontology...

In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

produce a data.frame of features relevant to a Cell Ontology class

Description

produce a data.frame of features relevant to a Cell Ontology class

Usage

CLfeats(ont, tag = "CL:0001054", pr, go)

Arguments

ont	instance of ontologyIndex ontology
tag	character(1) a CL: class tag
pr	instance of ontologyIndex PRO protein ontology
go	instance of ontologyIndex GO gene ontology

Value

a data.frame instance

Note

This function will look in the intersection_of and has_part, lacks_part components of the CL entry to find properties asserted of or inherited by the cell type identified in 'tag'. As of 1.19, this function does not look in global environment for ontologies. We use 2021 versions in the examples because some changes in ontologies omit important relationships; revisions to package code after 1.19.4 will attempt to address these.

Examples

cl = getOnto("cellOnto", year_added="2021")
pr = getOnto("Pronto", "2021")  # legacy tag, for 2022 would be PROnto
go = getOnto("goOnto", "2021")
CLfeats(cl, tag="CL:0001054", pr=pr, go=go)

vjcitn/ontoProc documentation built on March 23, 2024, 7:23 a.m.