guildifyR: A package for accessing GUILDify v2.0 server via R

Methods to connect GUILDify v2.0 web server to retrieve genes associated with a given phenotype and to apply interactome-based prioritization of genes in the species / tissue specific protein interaction network.

Requirements

• Depends:

  • R (>= 3.0.2)
  • magrittr

• Imports:

  • httr
  • rvest

Generating man files / installation using roxygen / devtools

library(devtools)
#setwd("guildifyR")
document()

Generating manual using Rd2pdf

R CMD Rd2pdf --pdf --title='guildifyR' -o guildifyR.pdf man/*.Rd

Generating tar.gz archieve

tar cvzf guildifyR.tgz --exclude .git guildifyR/

Install from tgz file

R CMD INSTALL guildifyR.tgz

Install from source using devtools

library(devtools)
setwd("..")
install("guildifyR")

Install from GitHub repository using devtools

library(devtools)
install_github("emreg00/guildifyR") 

Example query and retrieve results code

library(guildifyR)

# Parameters
species="9606"
tissue="all"
network.source="BIANA"

# Query and run using keyword Alzheimer 
result.table = query("alzheimer", species, tissue, network.source)
job.id = submit.job(result.table, species, tissue, network.source, list(netscore=T, repetitionSelector=3, iterationSelector=2))

# Retrieve results (once completed)
result = retrieve.job(job.id)

# Query and run using keyword lung neoplasms 
result.table = query("lung neoplasms", species, tissue, network.source)
job.id2 = submit.job(result.table, species, tissue, network.source, list(netscore=T, repetitionSelector=3, iterationSelector=2))

# Check overlap between the two results (once the runs are completed)
result = retrieve.overlap(job.id, job.id2)