ctmarks: app to review molecular properties of cell types via cell...

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

app to review molecular properties of cell types via cell ontology

Description

app to review molecular properties of cell types via cell ontology

Usage

ctmarks(cl, pr, go)

Arguments

cl	an import of a Cell Ontology (or extended Cell Ontology) in ontology_index form
pr	an import of a Protein Ontology in ontology_index form
go	an import of a Gene Ontology in ontology_index form

Value

a data.frame with features for selected cell types

Note

Prototype of harvesting of cell ontology by searching has_part, has_plasma_membrane_part, intersection_of and allied ontology relationships. Uses shiny. Can perform better if getPROnto() and getGeneOnto() values are in .GlobalEnv as pr and go respectively.

Examples

if (interactive()) {
   co = getOnto("cellOnto", year_added="2023")  # has plasma membrane relations
   go = getOnto("goOnto", "2023")
   pr = getOnto("Pronto", "2021") # peculiar tag used in legacy, would be PROnto with 2022
   ctmarks(co, go, pr)
}

vjcitn/ontoProc documentation built on Nov. 22, 2024, 6:11 p.m.