README.md

In bmbroom/ISB-CGC-utils: Utilities for Creating NG-CHMs using the ISB CGC

ISB-CGC-utils

This repository provides a small R package of example functions for simplifying the creation of Next-Generation Clustered Heat Maps (NG-CHMs) using the ISB CGC cloud pilot.

The rstudio-isb-ngchm-demo repository provides an example RStudio system extended with this package (and the NG-CHM R package).

Usage

Load the NGCHM package and create a connection to the desired NG-CHM server(s):

> library(NGCHM)
> chmCreateManagedServer('cloud','name-of-ngchm-instance','external-ip-of-ngchm-instance')

The example shows how to connect to the managed NG-CHM server created by the ngchm-system-one system in a cloud environment.

Specify the name of the google cloud project you will use and load the ISBCHM package:

> options(cloudproject='name-of-your-google-cloud-project')
> library(ISBCHM)

Obtain data for approximately 410 cancer-related genes and 545 prostate cancer samples from the ISB CGC cloud and create an NG-CHM:

> chm <- demoCHM()

Display the NG-CHM in the viewer pane of your RStudio console:

> plot(chm)

You can expand the viewer pane to a whole browser tab/window. You can also display the NG-CHM directly in a browser tab/window:

> browseURL(chmGetURL(chm))

bmbroom/ISB-CGC-utils documentation built on May 12, 2019, 10:24 p.m.