sym2CellOnto: use Cell Ontology and Protein Ontology to identify cell-type...

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

use Cell Ontology and Protein Ontology to identify cell-type defining conditions in which a given gene is named

Description

use Cell Ontology and Protein Ontology to identify cell-type defining conditions in which a given gene is named

Usage

sym2CellOnto(sym, cl, pr)

Arguments

sym	gene symbol, must be used in protein ontology as a PRO:DNx exact match token
cl	result of getOnto("cellOnto")
pr	result of getOnto("PROnto")

Value

DataFrame if any hits are found. A field 'cond' abbreviates the identified conditions: (has/lacks)PMP (plasma membrane part) (hi/lo)PMAmt (plasma membrane amount), (has/lacks)Part.

Note

Currently just checks for *plasma_membrane_part, *plasma_membrane_amount, and *Part conditions.

Examples

if (!exists("cl")) cl = getOnto("cellOnto")
if (!exists("pr")) pr = getOnto("PROnto")
sym2CellOnto("ITGAM", cl, pr)
sym2CellOnto("FOXP3", cl, pr)

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