PPIFromString: PPI network from STRING

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

Description

Constructing protenin-protein interaction network from STRING database, when STRING contains gene names from gene expression platform, like Saccharomyces cerevisiae

Usage

PPIFromString(pvalues, GeneNames, STRINGfilename, STRINGTheta = 0, savename)

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
STRINGfilename	The file downloaded from STRING, like 4932.protein.links.v10.txt
STRINGTheta	The threshold for PPI edges selections when using STRING
savename	The file to save filtered gene symbols and network edgelist

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.