A function to generate the protein-protein interaction (ppi) induced (un)directed graph

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Description

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

Usage

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

Arguments

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).

Value

An instance of the class graph.

Author(s)

T Chiang

Examples

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

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