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

In vjcitn/ontoProc: processing of ontologies of anatomy, cell lines, and so on

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

Description

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

Usage

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

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

vjcitn/ontoProc documentation built on Nov. 22, 2024, 6:11 p.m.