produce a data.frame of features relevant to a Cell Ontology class
CLfeats(ont, tag = "CL:0001054", pr, go)instance of ontologyIndex ontology
character(1) a CL: class tag
instance of ontologyIndex PRO protein ontology
instance of ontologyIndex GO gene ontology
a data.frame instance
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.
cl = getOnto("cellOnto", year_added="2021")
#> loading from cache
pr = getOnto("Pronto", "2021") # legacy tag, for 2022 would be PROnto
#> loading from cache
go = getOnto("goOnto", "2021")
#> loading from cache
CLfeats(cl, tag="CL:0001054", pr=pr, go=go)
#> no recognized predicate references for CL:0000576
#> no recognized predicate references for CL:0000766
#> no recognized predicate references for CL:0000738
#> no recognized predicate references for CL:0000988
#> no recognized predicate references for CL:0000219
#> no recognized predicate references for CL:0000003
#> tag prtag cond
#> 1 CL:0001054 PR:000001002 lacksPMP
#> 2 CL:0001054 PR:000001020 lacksPMP
#> 3 CL:0001054 PR:000001289 lacksPMP
#> 4 CL:0000000 GO:0005634 hasPart
#> 5 CL:0000000 GO:0005634 hasPart
#> entity SYMBOL
#> 1 CD19 molecule CD19
#> 2 CD3 epsilon CD3E
#> 3 membrane-spanning 4-domains subfamily A member 1 MS4A1
#> 4 nucleus <NA>
#> 5 nucleus <NA>
#> name
#> 1 CD14-positive monocyte
#> 2 CD14-positive monocyte
#> 3 CD14-positive monocyte
#> 4 cell
#> 5 cell