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


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Documentation for package ‘ontoProc’ version 1.2.1

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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'
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
getEFOOnto 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
makeSelectInput generate a selectInput control for an ontologyIndex slice
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
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