incgraph-scripts

This repository contains the code and the data required to reproduce the results shown in the IncGraph manuscript (under review).

Data

Finally, you should uncompress the zip files at data/genie3/expression/*.7z.

Install

A few packages need to be installed.

install.packages("devtools")
install.packages("incgraph")
devtools::install_github("rcannood/GENIE3")

Cluster

The PRISM package allows for easy communication between Rstudio and a gridengine-based cluster. For this, you will need to set up an openssh connection with your own gridengine cluster. If you do not wish to make use of PRISM's qsub_lapply, you can change all qsub_lapply's in the code with regular lapply's or parallelMap's.

devtools::install_github("rcannood/PRISM") 

conf <- PRISM::create_qsub_config(
  remote = "yourremote",
  local_tmp_path = "/home/yourusername/.r2gridengine",
  remote_tmp_path = "/home/yourusername/.r2gridengine"
)
PRISM::set_default_qsub_config(conf)