cellTypeToGO: utilities for approximate matching of cell type terms to GO...

Description Usage Arguments Value Note Examples

View source: R/termProc.R

Description

utilities for approximate matching of cell type terms to GO categories and annotations

Usage

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cellTypeToGO(celltypeString, gotab, ...)

cellTypeToGenes(celltypeString, gotab, orgDb, cols = c("ENSEMBL",
  "SYMBOL"), ...)

Arguments

celltypeString

character atom to be used to search GO terms using

gotab

a data.frame with columns GO (goids) and TERM (term strings) agrep

...

additional arguments to agrep

orgDb

instances of orgDb

cols

columns to be retrieved in select operation

Value

data.frame

data.frame

Note

Very primitive, uses agrep to try to find relevant terms.

Examples

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data(allGOterms)
library(org.Hs.eg.db)
head(cellTypeToGO("serotonergic neuron", allGOterms))
head(cellTypeToGenes("serotonergic neuron", allGOterms, org.Hs.eg.db))

ontoProc documentation built on Nov. 1, 2018, 4:29 a.m.