get_ppi_for_molecules: get_ppi_for_molecules

In humayun2017/SPAGI: SPAGI: Signalling Pathway Analysis for putative Gene regulatory network Identification

Description

This function gets the PPI data from STRINGdb for the protein molecules provided.

Usage

get_ppi_for_molecules(RP.protein, KN.protein, TF.protein, species,
  score = 700)

Arguments

RP.protein	A vector containg the receptor (RP) proteins.
KN.protein	A vector containg the kinase (KN) proteins.
TF.protein	A vector containg the transcription factor (TF) proteins.
species	The species name, either "hsapiens" or "mmusculus".
score	An interger value for the STRINGdb PPI score threshold cutoff. Default is 700.

Details

This function gets the PPI data from STRINGdb for the protein molecules provided.

Value

This function returns a data frame of the PPI for the molecules.

Examples

## Need two folder at working directory for downloading stringdb files for each species - stringdb_mouse, stringdb_human.
## It takes some time to download the data, and then can reuse the downloaded data.
## Here we will use RP.protein, KN.protein, TF.protein protein parameters. These data are automatically loaded with the package. You can modify these parameters.
## And we will use the species as "mmusculus".

## Get PPI data for the protein molecules of species "mmusculus".
mm.ppi<-get_ppi_for_molecules(RP.protein, KN.protein, TF.protein, species="mmusculus")
head(mm.ppi)

humayun2017/SPAGI documentation built on May 13, 2019, 1:35 p.m.