Construct the GO graph given a set of leaves.

Description

Given one or more GO identifiers (which indicate the leaves in the graph) and a set of mappings to the less specific sets of nodes this function will construct the graph that includes that node and all children down to the root node for the ontology.

Usage

oneGOGraph(x, dataenv)
GOGraph(x, dataenv)

Arguments

Details

For any set of GO identifiers (from a common ontology) we define the induced GO graph to be that graph, based on the DAG structure (child - parent) of the GO ontology of terms, which takes the most specific set of GO terms that apply (for that ontology) and then joins these to all less specific terms. These functions help construct such graphs.

Value

The induced GO graph (or NULL) for the given GO identifier.

Author(s)

R. Gentleman

See Also

makeGOGraph

Examples

 library("GO.db")
 g1 <- oneGOGraph("GO:0003680", GOMFPARENTS)
 g2 <- oneGOGraph("GO:0003701", GOMFPARENTS)
 g3 <- join(g1, g2)

 g4 <- GOGraph(c("GO:0003680", "GO:0003701"), GOMFPARENTS)
if( require("Rgraphviz") && interactive() )
  plot(g3)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(GOstats)
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, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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

Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:S4Vectors':

    expand

Loading required package: graph


Attaching package: 'GOstats'

The following object is masked from 'package:AnnotationDbi':

    makeGOGraph

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GOstats/oneGOGraph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: oneGOGraph
> ### Title: Construct the GO graph given a set of leaves.
> ### Aliases: oneGOGraph GOGraph
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
>  library("GO.db")
>  g1 <- oneGOGraph("GO:0003680", GOMFPARENTS)
>  g2 <- oneGOGraph("GO:0003701", GOMFPARENTS)
>  g3 <- join(g1, g2)
> 
>  g4 <- GOGraph(c("GO:0003680", "GO:0003701"), GOMFPARENTS)
> #if( require("Rgraphviz") && interactive() )
>   plot(g3)

Attaching package: 'Rgraphviz'

The following objects are masked from 'package:IRanges':

    from, to

The following objects are masked from 'package:S4Vectors':

    from, to

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>