Code and Data for 2016 PSB publication

####Note: This github reppository contains most code and some data used by this project. Limited by file size, some big datasets and algorithms/softwares (all open to public) are not uploaded. Detailed information will be provided upon request.

1 ./data

• contains some datasets used by this project
• ./mental-disorder-years-threshold-3percent
  • contains the processed data from CT.GOV
• ./pubmed_matched
  • show matched diseases for both CT.GOV and PubMed datasets (automatic matching)

2 ./script

• all scripts (mainly python and R) used by this project
• rawDataProcessing.py main script
• ./pylib python libraries used in the project
• ./rlib R library used in the project (for Rscript user, one can import the rlib.Rproj to run all R code)

3 ./result

• some (middle) results
• ./Comparison_in_ex all: results while compare CT.GOV inclusion/exclusion criteria
• ./Comparison_pubmed_ex: results while compare CT.GOV exclusion criteria with PubMed data
• ./network_In_Ex_Pubmed: network analysis results
• ./match_pubmed: matched diseases for both CT.GOV and PubMed datasets (semi-automatic matching with manual corrections)

4 ./REF

• all references used in the paper

mapDiseaseName: map Did and Disease Name (optional) get_cde_st_table(): get CDE-ST table for all cytoscapePrepare[N](): prepare for cytoscape file (from inpath files using R)

The programs in this folder is used to analysis generated by previous rawDataProcessing process.

Take the following steps:

1. rscript CDE_unique_analysis.R #source

2. source('./ST_analysis (original).R') #can not be finished in one program

• group=in
• group=ex

source("./networkAnalysis.R")

There are duplicated entries in the edgelist:pubmed

see overlap

Rscript Comparison_overlap.R, source won't plot, need run as bash

see top table FOR BOTH OVERAL AND PER DISEASE

source('./Comparison_topCEF.R)

For any question or request, please contact me at handongma.work at gmail.com

or

Chunhua Weng's Lab