fiveP-ml

This repo contains the scripts to obtain the '5 Ps' of a number of input genes: protein complex, protein family, paralogues, pathways, and protein-protein interactions. The output is a data frame with all protein coding genes and a binary score (0 or 1) describing whether each gene is in the same 'P' as any of the input genes.

Installation

Install devtools

install.packages("devtools")

Install dependencies

if (!requireNamespace("tidyverse", quietly = TRUE))
install.packages("tidyverse")

if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")

if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

if (!requireNamespace("STRINGdb", quietly = TRUE)) {
BiocManager::install("STRINGdb") }

if (!requireNamespace("biomaRt", quietly = TRUE)) {
BiocManager::install("biomaRt") }

Install package

devtools::install_github("martadelfino/fiveP-ml")

Load package

library(fivePml)