Scripts and data for re-generating results from the TDM manuscript.

Use run_experiments.R to regenerate the analyses from Thompson et al..

We are using Git Large File Storage to store gene expression data. You will need to install the client if you do not already have it installed. Once you install the client, run git lfs pull in the clone to retrieve the datasets. After retrieving the datasets, using run_experiments.R will regenerate the results.

This requires the following R & Bioconductor packages be installed (see check_installs.R for confirmation of installation):

* ggplot2
* reshape2
* Hmisc
* data.table
* scales
* sdcMicro
* flexclust
* fpc
* corrplot
* ape
* cluster
* plyr
* dplyr
* devtools
* quantro
* preprocessCore
* gridExtra
* huge
* caret
* limma
* glmnet
* e1071
* stringr
* gdata
* binr
* cowplot

One github package is required:

library("devtools")
install_github(repo = "quantroSim", username = "stephaniehicks")

We have created an R script which will call 'require' on each of these packages to make sure they are installed: check_installs.R

By default, all input data is expected to be in this local directory and normalized data and figure output is within this directory as well. If you'd like to change this behavior, modify "directories.R".

Acknowledgements: This research is funded in part by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4552 to CSG. JT is a Neukom Graduate Fellow supported by the William H. Neukom 1964 Institute for Computational Science. This work was supported in part by P20 GM103534, P30 CA023108 and UL1 TR001086 from the NIH and an American Cancer Society Research Grant, #IRG-82-003-27. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.