genBPGraph: A function to generate the protein-protein interaction (ppi)...
In ppiStats: Protein-Protein Interaction Statistical Package

Description Usage Arguments Value Author(s) Examples

This function will take the ppi data and generate instance of the class graph.

1	genBPGraph(bpMat, directed=TRUE, bp=TRUE)

`bpMat`	An adjacency matrix of PPI. If the matrix is obtained by empirical data, or bait to prey, then the rows are indexed by the baits and the columns indexed by the preys. If the rownames are not the same as the column names (i.e. a generic bait to prey matrix) the argument bp must be set to TRUE.
`directed`	A logical - if TRUE, the object will be a directed graph rather than an ordinary graph. For bait to prey interactions, this parameter must always be set to TRUE.
`bp`	A logical - if TRUE, it signifies that the adjacency matrix is a bait to prey empirically derived matrix so that the bait population (rownames) is usually different from the prey population (colnames).

An instance of the class graph.

T Chiang

library(ppiData)
library(graph)
data(y2hSysGW)
eg=y2hSysGW[[3]]
egMat = bpMatrix(eg)
genBPGraph(egMat)

Loading required package: ScISI
Loading required package: GO.db
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, 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: RpsiXML
Loading required package: annotate
Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

Loading required package: RBGL
Loading required package: hypergraph
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'

Attaching package: 'RpsiXML'

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

    members

Loading required package: apComplex

Loading required package: lattice
Loading required package: ppiData
A graphNEL graph with directed edges
Number of Nodes = 74 
Number of Edges = 115