sym2CellOnto {ontoProc}R Documentation

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 getCellOnto()

pr

result of getPROnto()

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 = getCellOnto()
if (!exists("pr")) pr = getPROnto()
sym2CellOnto("ITGAM", cl, pr)
sym2CellOnto("FOXP3", cl, pr)

[Package ontoProc version 1.14.0 Index]