construct_nlocal

A data frame containing the experimental data.

input

Integrated PPI database, either <code>Biogrid</code> or <code><a rd-options="" href="/link/HPRD?package=ProNet&version=1.0.0" data-mini-rdoc="ProNet::HPRD">HPRD</a></code>.

This parameter indicates the biological species to which analyzable PPI data is related; currently <code>human</code> for "Homo sapiens" and <code>ath</code> for "Arabidopsis thaliana" are available.

species

The ID type of the biological genes or proteins, possible values are <code>Entrez gene</code> and <code>Gene symbol</code> when <code>db</code> is <code>Biogrid</code>, or <code>Gene symbol</code> when <code>db</code> is <code><a rd-options="" href="/link/HPRD?package=ProNet&version=1.0.0" data-mini-rdoc="ProNet::HPRD">HPRD</a></code>.

ID.type

This parameter indicates how many hierarchy are included in the network, currently it can be <code>0</code>, <code>1</code> or <code>2</code>. Default value is <code>1</code>.

hierarchy


Construction a network from integrated PPI database.


High-throughput experiments are now widely used in biological researches, which improves both the quality and quantity of omics data. Network-based presentation of these data has become a popular way in data analyses. This package mainly provides functions for biological network construction, visualization and analyses. Networks can be constructed either from experimental data or from a set of proteins and integrated PPI database. Based on them, users can perform traditional visualization, along with the subcellular localization based ones for Homo sapiens and Arabidopsis thaliana. Furthermore, analyses including topological statistics, functional module clustering and go profiling can also be achieved.

XiaYu Xia

ProNet

Biological Network Construction, Visualization and Analyses

construct_nlocal function

Integrated PPI database, either <code>Biogrid</code> or <code><a rd-options='' href='HPRD'>HPRD</a></code>.

The ID type of the biological genes or proteins, possible values are <code>Entrez gene</code> and <code>Gene symbol</code> when <code>db</code> is <code>Biogrid</code>, or <code>Gene symbol</code> when <code>db</code> is <code><a rd-options='' href='HPRD'>HPRD</a></code>.

construct_nlocal: Non-local network construction

Description

Usage

Arguments

Value

See Also

Examples