processing of ontologies of anatomy, cell lines, and so on


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Documentation for package ‘ontoProc’ version 1.8.1

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allGOterms allGOterms: data.frame with ids and terms
c-method combine TermSet instances
cellTypeToGenes utilities for approximate matching of cell type terms to GO categories and annotations
cellTypeToGO utilities for approximate matching of cell type terms to GO categories and annotations
children_TAG generate a TermSet with siblings of a given term, excluding that term by default
cleanCLOnames obtain named character vector of terms from Cell Line Ontology, omitting obsolete and trailing 'cell'
CLfeats produce a data.frame of features relevant to a Cell Ontology class
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
getCellLineOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getCellOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getCellosaurusOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getChebiLite load ontologies that may include non-ascii strings and therefore cannot be in data folder
getChebiOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getDiseaseOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getEFOOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getGeneOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getHCAOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getLeavesFromTerm obtain childless descendents of a term (including query)
getOncotreeOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getPATOnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getPROnto load ontologies that may include non-ascii strings and therefore cannot be in data folder
getUBERON_NE load ontologies that may include non-ascii strings and therefore cannot be in data folder
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
label_TAG generate a TermSet with siblings of a given term, excluding that term by default
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
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
packDesc2019 packDesc2019: overview of ontoProc resources
PROSYM PROSYM: HGNC symbol synonyms for PR (protein ontology) entries identified in Cell Ontology
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
seur3kTab tabulate the basic outcome of PBMC 3K tutorial of Seurat
show manage ontological data with tags and a DataFrame instance
show-method manage ontological data with tags and a DataFrame instance
siblings_TAG generate a TermSet with siblings of a given term, excluding that term by default
stopWords stopWords: vector of stop words from xpo6.com
sym2CellOnto use Cell Ontology and Protein Ontology to identify cell-type defining conditions in which a given gene is named
TermSet-class manage ontological data with tags and a DataFrame instance