PPIFromStringEnsembl: PPI network from STRING and Ensembl

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

Description

Constructing protenin-protein interaction network from STRING database, when protein name is needed for mapping with gene name from Ensembl

Usage

PPIFromStringEnsembl(pvalues, GeneNames, STRINGfilename, STRINGTheta = 0,
  Ensemblfilename, 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 9606.protein.links.v10.txt
STRINGTheta	The threshold for PPI edges selections when using STRING
Ensemblfilename	The file downloaded from ensembl (Customise your download), like mart_export.txt, first column is Associated Gene Name like MT-ND1, second column is Ensembl Protein ID like ENSP00000354687
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.