makeGOGraph: A convenience function to generate graphs based on the GO.db...

In AnnotationDbi: Manipulation of SQLite-based annotations in Bioconductor

Description

makeGOGraph is a function to quickly convert any of the three Gene Ontologies in GO.db into a graphNEL object where each edge is given a weight of 1.

Usage

  makeGOGraph(ont = c("bp","mf","cc"))

Arguments

ont	Specifies the ontology: "cc", "bp" or "mf".

Author(s)

Marc Carlson

See Also

GOTerms

Examples

  ## makes a GO graph from the CC ontology 
  f <- makeGOGraph("cc")

Example output

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, cbind, colMeans, colSums, colnames, 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: graph
Loading required package: GO.db

AnnotationDbi documentation built on Nov. 8, 2020, 4:50 p.m.