getOntology: Get GO terms for a specified ontology

In annotate: Annotation for microarrays

Description

Find the subset of GO terms for the specified ontology, for each element of the supplied list of associations. The input list is typically from one of the chip-specific meta-data files.

Usage

getOntology(inlist, ontology=c("MF", "BP", "CC"))

Arguments

inlist	A list of GO associations
ontology	The name of the ontology you want returned.

Details

The input list should be a list of lists, each element of inlist is itself a list containing the information that maps from a specified ID (usually LocusLink) to GO information. Each element of the inner list is a list with elements GOID, Ontology and Evidence.

Value

A list of the same length as the input list. Each element of this list will contain a vector of GOIDs for those terms that match the requested ontology.

Author(s)

R. Gentleman

See Also

getEvidence, dropECode

Examples

 library("hgu95av2.db")
 bb <- hgu95av2GO[["39613_at"]]
 getOntology(bb)
 sapply(bb, function(x) x$Ontology)

Example output

Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, 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:base’:

    expand.grid

Loading required package: XML
Loading required package: org.Hs.eg.db


[1] "GO:0004571" "GO:0005509" "GO:0015923"
GO:0006486 GO:0006491 GO:1904381 GO:0000139 GO:0000139 GO:0005783 GO:0005793 
      "BP"       "BP"       "BP"       "CC"       "CC"       "CC"       "CC" 
GO:0005794 GO:0005829 GO:0016020 GO:0016021 GO:0070062 GO:0004571 GO:0005509 
      "CC"       "CC"       "CC"       "CC"       "CC"       "MF"       "MF" 
GO:0015923 
      "MF" 

annotate documentation built on Nov. 8, 2020, 8:14 p.m.