PPIFromBioGRID: PPI network from BioGRID

In fairmiracle/PPINet: Protenin-protein interaction network construction and module identification

Description

Constructing protenin-protein interaction network from BioGRID database

Usage

PPIFromBioGRID(pvalues, GeneNames, BioGRIDfilename, savename, column1, column2)

Arguments

pvalues	A N-dimensional vector of gene expression level, processed by limma
GeneNames	A N-dimensional vector of gene symbols, pre-filtering by expression profiles
BioGRIDfilename	The file downloaded from BioGRID, like BIOGRID-ORGANISM-Homo_sapiens-3.4.138.tab.txt
savename	The file to save filtered gene symbols and network edgelist
column1	Source column in BioGRID file, for Saccharomyces_cerevisiae column1=1 and for Homo_sapiens column1=3
column2	Target column in BioGRID file, for Saccharomyces_cerevisiae column2=2 and for Homo_sapiens column3=4

Value

net two or three column edge list for NetSimplify or PPIplot and p-values vector.

Author(s)

Dong Li, [e-mail]

fairmiracle/PPINet documentation built on May 16, 2019, 9:59 a.m.