construction: Network construction

In ProNet: Biological Network Construction, Visualization and Analyses

Description

Construction a network from experimental data or integrated PPI database.

Usage

construction(input, local.net = FALSE, node.attribute = NULL,
  db = c("Biogrid", "HPRD"), species = c("human", "ath"),
  ID.type = c("Gene symbol", "Entrez Gene"), hierarchy = 1)

Arguments

input	A data frame containing the experimental data.
local.net	Logical value, indicating whether to construct a network from experimental data (if TRUE) or not (if FLASE). Default value is FALSE.
node.attribute	A data frame containing node attributes. Default value is NULL.
db	Integrated PPI database, either Biogrid or HPRD.
species	This parameter indicates the biological species to which analyzable PPI data is related; currently human for "Homo sapiens" and ath for "Arabidopsis thaliana" are available.
ID.type	The ID type of the biological genes or proteins, possible values are Entrez gene and Gene symbol when db is Biogrid, or Gene symbol when db is HPRD.
hierarchy	This parameter indicates how many hierarchy are included in the network, currently it can be 0, 1 or 2. Default value is 1.

Value

A network in igraph format.

See Also

construct_local, construct_nlocal

Examples

## Construction a local network.
local<-data.frame(1:5,2:6)
attribute<-data.frame(1:6,c(2.2,5.3,1.2,4.5,6.2,0.6))
net<-construction(input=local,local.net=TRUE,node.attribute=attribute)
## Construction a network from the human HPRD database.
nlocal<-data.frame(c("DVL1","DVL2","DVL3"))
net<-construction(input=nlocal,db="HPRD",species="human",ID.type="Gene symbol",hierarchy=1)

Example output

Loading required package: Rcpp
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: MCL
Loading required package: linkcomm
Loading required package: RColorBrewer

Welcome to linkcomm version 1.0-11

For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))

ProNet documentation built on May 30, 2017, 2:02 a.m.