Source the Protein-Protein interaction in STRING database

This function is able to use a list of Transcription Factors(TF) of interest to source the Protein-Protein interactions (PPI)in STRING database

source.PPI(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()$major=="3"){PPI <- source.PPI(TF, STRING.version="10", 
species.index=83332, score_threshold=0)}
if(R.Version()$major=="4"){PPI <- source.PPI(TF, STRING.version="11", 
species.index=83332, score_threshold=0)}
# write out locally then can be used in \code{\link{panda.py}}.