Function reference • ontoProc

All functions
`CLfeats()`	produce a data.frame of features relevant to a Cell Ontology class
`PROSYM`	PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
`show(<TermSet>)`	manage ontological data with tags and a DataFrame instance
`allGOterms`	allGOterms: data.frame with ids and terms
`ancestors()`	retrieve ancestor 'sets'
`ancestors_names()`	obtain list of names of a set of ancestors
`bind_formal_tags()`	add mapping from informal to formal cell type tags to a SummarizedExperiment colData
`c(<TermSet>)`	combine TermSet instances
`cellTypeToGO()` `cellTypeToGenes()`	utilities for approximate matching of cell type terms to GO categories and annotations
`children_names()`	obtain list of names of a set of subclasses/children
`cleanCLOnames()`	obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell'
`common_classes()`	list and count samples with common ontological annotation in two SEs
`connect_classes()`	connect ontological categories between related, annotated SummarizedExperiments
`ctmarks()`	app to review molecular properties of cell types via cell ontology
`cyclicSigset()`	as in Bakken et al. (2017 PMID 29322913) create gene signatures for k cell types, each of which fails to express all but one gene in a set of k genes
`demoApp()`	demonstrate the use of makeSelectInput
`dropStop()`	dropStop is a utility for removing certain words from text data
`fastGrep()`	some fields of interest are lists, and grep per se should not be used -- this function checks and uses grep within vapply when appropriate
`findCommonAncestors()`	Find common ancestors
`getChebiLite()` `getCellosaurusOnto()` `getUBERON_NE()` `getChebiOnto()` `getOncotreeOnto()` `getDiseaseOnto()` `getGeneOnto()` `getHCAOnto()` `getPROnto()` `getPATOnto()` `getMondoOnto()` `getSIOOnto()`	basic getters in old style, retained 2023 for deprecation interval
`getLeavesFromTerm()`	obtain childless descendents of a term (including query)
`getOnto()`	get the ontology based on a short tag and year
`get_classes()`	return a generator with ontology classes
`get_ordo_owl_path()`	decompress ordo owl file
`humrna`	humrna: a data.frame of SRA metadata related to RNA-seq in humans
`improveNodes()`	inject linefeeds for node names for graph, with textual annotation from ontology
`labels(<owlents>)`	retrieve labels with names
`ldfToTerms()`	use output of cyclicSigset to generate a series of character vectors constituting OBO terms
`liberalMap()`	Produce a data.frame with a set of naive terms mapped to all matching ontology ids and their formal terms
`makeSelectInput()`	generate a selectInput control for an ontologyIndex slice
`make_graphNEL_from_ontology_plot()`	obtain graphNEL from ontology_plot instance of ontologyPlot
`map2prose()`	use prose terminology with output of connect_classes
`mapOneNaive()`	use grep or agrep to find a match for a naive token into ontology
`minicorpus`	minicorpus: a vector of annotation strings found in 'study title' of SRA metadata.
`nomenCheckup()`	repair nomenclature mismatches (to curated term set) in a vector of terms
`onto_plot2()`	high-level use of graph/Rgraphviz for rendering ontology relations
`onto_roots()`	list parentless nodes in ontology_index instance
`owl2cache()`	cache an owl file accessible via URL
`packDesc2019`	packDesc2019: overview of ontoProc resources
`packDesc2021`	packDesc2021: overview of ontoProc resources
`packDesc2022`	packDesc2022: overview of ontoProc resources
`packDesc2023`	packDesc2023: overview of ontoProc resources
`parents()`	retrieve is_a
`plot.owlents()`	visualize ontology selection via onto_plot2, based on owlents
`print(<owlents>)`	short printer
`recognizedPredicates()`	enumerate ontological relationships used in ontoProc utilities
`secLevGen()`	simple generation of children of 'choices' given as terms, returned as TermSet
`selectFromMap()`	select a set of elements from a term 'map' and return a contribution to a data.frame
`setup_entities()`	construct owlents instance from an owl file
`seur3kTab()`	tabulate the basic outcome of PBMC 3K tutorial of Seurat
`siblings_TAG()` `label_TAG()` `children_TAG()`	generate a TermSet with siblings of a given term, excluding that term by default
`stopWords`	stopWords: vector of stop words from xpo6.com
`[`(<owlents>)	subset method
`subclasses()`	retrieve subclass entities
`subset_descendants()`	subset a SummarizedExperiment to which ontology tags have been bound using 'bind_formal_tags', obtaining the 'descendants' of the class of interest
`sym2CellOnto()`	use Cell Ontology and Protein Ontology to identify cell-type defining conditions in which a given gene is named
`url_ok()`	check that a URL can get a 200 for a HEAD request
`valid_ontonames()`	give a vector of valid 'names' of ontoProc ontologies

Reference

All functions