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

Note

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

Examples

library(org.Hs.eg.db)
#> Loading required package: AnnotationDbi
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> 
#> Attaching package: ‘BiocGenerics’
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
#>     union, unique, unsplit, which.max, which.min
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: IRanges
#> Loading required package: S4Vectors
#> 
#> Attaching package: ‘S4Vectors’
#> The following object is masked from ‘package:utils’:
#> 
#>     findMatches
#> The following objects are masked from ‘package:base’:
#> 
#>     I, expand.grid, unname
#> 
data(allGOterms)
head(cellTypeToGO("serotonergic neuron", allGOterms))
#>             GOID                                        TERM
#> 18623 GO:0036515           serotonergic neuron axon guidance
#> 18625 GO:0036517 chemoattraction of serotonergic neuron axon
#> 18627 GO:0036519  chemorepulsion of serotonergic neuron axon
head(cellTypeToGenes("serotonergic neuron", allGOterms, org.Hs.eg.db))
#> 'select()' returned 1:many mapping between keys and columns
#>           GO EVIDENCE ONTOLOGY         ENSEMBL  SYMBOL
#> 1 GO:0036515      ISS       BP ENSG00000008300  CELSR3
#> 2 GO:0036515      ISS       BP ENSG00000104290    FZD3
#> 3 GO:0036515      IEA       BP ENSG00000243232 PCDHAC2
#> 4 GO:0036515      IEA       BP ENSG00000291668 PCDHAC2
#> 5 GO:0036515      ISS       BP ENSG00000162738  VANGL2
#> 6 GO:0036517      ISS       BP ENSG00000114251   WNT5A