sourcePPI: Source the Protein-Protein interaction in STRING database

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

Source the Protein-Protein interaction in STRING database

Description

This function uses a list of Transcription Factors (TF) of interest to source the Protein-Protein interactions (PPI) from STRING database using all types of interactions not only the physical subnetwork Important: this function produces a simple unweighted network for tutorial purposes, and does not support weighted PPI edges for the moment. For more complex PPI network modeling, consider pulling the PPI network directly from STRINGdb directly or through their R package.

Usage

sourcePPI(TF, STRING.version = "10", species.index, ...)

Arguments

TF	a data frame with one column indicating the TF of interest
STRING.version	a numeric vector indicating the STRING version. Default valuve is 10
species.index	a numeric vector indicating NCBI taxonomy identifiers
...	any dditional arguments passed to

Value

A PPI data.frame which contains three columns: "from" and "to" indicating the direction of protein-protein interaction, and "score" indicating the interaction score between two proteins.

Examples

# the example motif file
motif_file_path <- system.file("extdata", "chip_matched.txt", package = "netZooR", mustWork = TRUE)
motif <- read.table(motif_file_path, sep="\t")
# create a TF data frame with one column
TF <-data.frame(motif[,1])
# create PPI data frame by searching in STRING version 10 
# and specifying specie to "Mycobacterium tuberculosis H37Rv".
# STRING verison 11 is only accessible to R 4.0.

if(R.Version()$major=="3"){PPI <- sourcePPI(TF, STRING.version="10", 
species.index=83332, score_threshold=0)}
if(R.Version()$major=="4"){PPI <- sourcePPI(TF, STRING.version="11", 
species.index=83332, score_threshold=0)}

# write out locally then can be used in \code{\link{pandaPy}}.

netZoo/netZooR documentation built on Oct. 16, 2024, 10:23 p.m.