sourcePPI: Source the Protein-Protein interaction in STRING database

In twangxxx/netZoo: Integrate methods: PANDA, LIONESS, CONDOR, ALPACA into one workflow.

Description

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

Usage

sourcePPI(TF, species.index, score_threshold = 0)

Arguments

TF	Data frame with one column indicating the TF of interest
species.index	Numeric vector indicating NCBI taxonomy identifiers
score_threshold	Numeric vector indicating the threshold for the combined scores of the interactions.Default to 0.

Value

A PPI data frame

Examples

# the example motif file
motif_file_path <- system.file("extdata", "chip.txt", package = "netZoo", mustWork = TRUE)
motif <- read.table(motif_file_path, sep="\t")
# create a TF data frame with one column
TF <- motif[,1]
# create PPI data frame
PPI <- sourcePPI(TF,species.index=83332, score_streshold=0)
# write locally then use in \code{\link{runPanda}}.

twangxxx/netZoo documentation built on May 17, 2019, 1:02 p.m.