list_genes: Returns the genes associated with a Gene Ontology

In GOexpress: Visualise microarray and RNAseq data using gene ontology annotations

Description

Given a Gene Ontology (GO) identifier represented in the dataset, returns a character vector listing the feature identifiers annotated to it.

Usage

list_genes(go_id, result, data.only=TRUE)

Arguments

go_id	A Gene Ontology (GO) identifier represented in the dataset.
result	The output of GO_analyse() or a subset of it obtained from subset_scores().
data.only	Whether to return only the feature identifiers present in the given dataset or alternatively returns all feature identifiers associated with the GO term in the Ensembl BioMart. Default is TRUE.

Value

A character vector listing the feature identifiers of the genes associated with the GO term.

Author(s)

Kevin Rue-Albrecht

See Also

Method GO_analyse.

Examples

# load the sample output data
data(AlvMac_results)

# List of genes associated with the GO term "toll-like receptor 4 signaling
# pathway"
list_genes(result=AlvMac_results, go_id="GO:0034142")

Example output

Loading required package: grid
Loading required package: Biobase
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

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

[1] "ENSBTAG00000047107" "ENSBTAG00000016683" "ENSBTAG00000016085"
[4] "ENSBTAG00000021377" "ENSBTAG00000019872" "ENSBTAG00000006240"
[7] "ENSBTAG00000015271"

GOexpress documentation built on Nov. 8, 2020, 7:45 p.m.