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

## Documentation for package ‘ontoProc’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'
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
getOncotreeOnto | 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
label_TAG | generate a TermSet with siblings of a given term, excluding that term by default
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
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
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
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
TermSet-class | manage ontological data with tags and a DataFrame instance