inducedGraph: The subgraph induced by a set of nodes.

In topGO: Enrichment Analysis for Gene Ontology

Description

Given a set of nodes (GO terms) this function is returning the subgraph containing these nodes and their ancestors.

Usage

inducedGraph(dag, startNodes)
nodesInInducedGraph(dag, startNodes)

Arguments

dag	An object of class graphNEL containing a directed graph.
startNodes	A character vector giving the starting nodes.

Value

An object of class graphNEL-class is returned.

Author(s)

Adrian Alexa

See Also

topGOdata-class, reverseArch,

Examples

data(GOdata)

## the GO graph
g <- graph(GOdata)
g

## select 10 random nodes
sn <- sample(nodes(g), 10)


## the subgraph induced by these nodes
sg <- inducedGraph(g, sn)
sg

Example output

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: graph
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: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

A graphNEL graph with directed edges
Number of Nodes = 777 
Number of Edges = 1557 
A graphNEL graph with directed edges
Number of Nodes = 88 
Number of Edges = 170 

topGO documentation built on Nov. 8, 2020, 6:55 p.m.