aqListGOIDs: List GO Identifiers by GO Ontology

In annotate: Annotation for microarrays

Description

This function returns a character vector of all GO identifiers in the specified ontologies: Biological Process (BP), Cellular Component (CC), Molecular Function (MF).

Usage

aqListGOIDs(ont)

Arguments

ont	A character vector specifying the two-letter codes of the ontologies from which all GO IDs will be retrieved. Entries must be one of "BP", "CC", or "MF".

Value

A character vector of GO IDs. The vector will contain all GO IDs in the GO ontologies specified by the ont argument.

Author(s)

Seth Falcon

Examples

## all GO IDs in BP
bp_ids = aqListGOIDs("BP")
length(bp_ids)

## all GO IDs in BP or CC
bp_or_cc_ids = aqListGOIDs(c("BP", "CC"))
length(bp_or_cc_ids)

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':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, 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

[1] 29586
[1] 33676

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