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

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

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)

Example output

Loading required package: ontologyIndex
DataFrame with 0 rows and 0 columns
DataFrame with 0 rows and 0 columns

ontoProc documentation built on Nov. 8, 2020, 4:49 p.m.