Disease Correlation Network (DCN) Analyser

Disease Correlation Network (DCN) Analyser is a pipeline of disease correlation analysis with retrospective matched cohort study design using Cox Proportional Hazards (Cox-PH) regression in combination of interactive network display using graph theory. It allows clinicians to explore the relationships between any statistically disease pairs easily by studying the network with customized filtering, rearranging the network and calculating all the possible path between disease pairs.

Prerequisities

• Linux or Mac OS
• python >= 3.7.0
• Rscript >= 3.5.0

Environment setup

If you do not have the above environment, please set it up via the following conda commands:

$ conda create --name DCN python=3.7 r=3.5 r-essentials
$ conda activate DCN

You can change the environment name DCN to anything you want.

After you are done, use the following code to deactivate.

$ conda deactivate

Citation

Lin H, Rong R, Gao X, Revanna K, Zhao M, Bajic P, Jin D, Hu C, Dong Q. Disease correlation network: a computational package for identifying temporal correlations between disease states from Large-Scale longitudinal medical records. JAMIA Open. 2019 Aug 23;2(3):353-359. doi: 10.1093/jamiaopen/ooz031. PMID: 31984368; PMCID: PMC6952009.

Live interactive network display for the paper: http://cbi.lumc.edu/disease/.

Install

To check out the source code, go to https://github.com/qunfengdong/DCN. To obtain the scripts and example DCN files, do the following:

$ git clone https://github.com/qunfengdong/DCN.git
$ cd DCN

After the github repository is cloned, you will find a folder named DCN. All the scripts and example data files will be included in it.

Test dataset

• A test dataset with those two files are available in test.tar.gz file. Please unzip it to view and go through the tutorial. Please note that the test dataset is simulated, thus its results are not a true reflection of scientific discovery.

$ tar zxvf test.tar.gz

1. View the example input file: cdc_first_test.tsv
2. View the example meta file: disease_code_test.tsv
3. View the time table: <DiseaseA>_<DiseaseB>.csv
4. View the survival curves of significant disease pairs based on Cox-PH regression: <DiseaseA>_<DiseaseB>.cox.survival.png and residual plot: <DiseaseA>_<DiseaseB>.cox.residual.png
5. Click on the index.html to view the result from example data.
6. View the survival curves of significant disease pairs based on Random Forest survival analysis: <DiseaseA>_<DiseaseB>.rf.survival.png

Running test

You will need to run the following codes inside the DCN folder to complete the test:

• Generate disease pairs

$ Rscript a0_generator.r -i ./test/cdc_first_test.tsv -m ./test/disease_code_test.tsv --outfolder ./example

• Analyze disease pairs using both Cox-PH and RF regression

$ Rscript a1_analyzer.r -m ./test/disease_code_test.tsv --inputfolder ./example --outputfolder ./example/output
$ Rscript a1_analyzer.r --method RF -m ./test/disease_code_test.tsv --inputfolder ./example --outputfolder ./example/output 

• Convert resulting Cox-PH regression results to json format for viewing

$ python a2_parse.py ./example/output/CoxPH.edge.csv

• Move results to the server folder

$ cp ./example/output/* web_server

Then just click-open the index.html inside web_server, you will see the network display. You can compare your results under the example folder with files in test folder.

NOTE: Files: CoxPH.edge.csv, RF.edge.csv, all.edges.csv.js, and all PNG files should be in the same folder as the index.html.

Quick start

• This suite of analysis includes five major parts:

1. Find all the exposed disease pairs;
2. Find all matched non-exposed disease pairs;
3. Perform Cox-PH regression on the two cohorts;
4. Perform Random Forest survival analysis on the two cohorts;
5. Visualize the results

• Step 1-2 is achieved by a0_generator.r, step 3-4 is achieved by a1_analyzer.r, and step 5 is achieved by a2_parse.py and index.html.

Required input files

• Before running any analysis using this pipeline, please make sure you have an input EMR file formatted as tab delimited with 6 columns in the order of patient ID, disease ID/name, disease diagnose date ([%Y-%m-%d] or [%Y/%m/%d]), age, gender, race. No header is needed. It should be something like the following:

P00001  62      2012-01-16      66      F       White
P00002  509     2009-01-12      68      M       African American
P00002  23      2014-11-07      73      M       African American
P00003  23      2015-07-20      78      M       White
P00007  44      2014-04-28      51      M       White
P00008  509     2010-07-12      54      M       White
P00015  509     2008-04-21      60      M       White
P00016  63      2008-03-16      83      F       White
P00017  23      2014-11-13      48      F       White
P00018  509     2011-07-03      76      M       African American
P00018  14      2012-09-20      77      M       African American
P00018  23      2014-01-09      79      M       African American
P00019  23      2015-01-09      89      M       White
P00020  14      2012-05-25      65      F       African American

• Meta file should be tab separated with header. The first column is the disease ID (should be consistant with the disease ID you have in the input data file), and second column is the disease name. Example of meta file:

id_col	name_long
14	Prostate Cancer
23	Glaucoma
29	Obesity
509	Med:Progestins
43	Acute Myeloid Leukemia
44	Vitiligo
59	Chalazion
62	Cirrhosis
63	Psoriasis
67	Sarcoidosis

Getting started

NOTE: You will need to enter your own file paths in the code below.

Step 1: a0_generator.r

Find all the exposed and matching non-exposed disease pairs.

• The default match finding criteria is: the matching subject is within 5 years of age difference (You can change this number using the argument: -y, --year), visit time is within 7 days (-d, --days) compared to the exposed counterparts, same race and gender.

• The default screen criteria for a disease is: the minimum number of subjects for a disease is 100 (--minn), while the maximum is 10000 (--maxn), and the minimum number of disease A to disease B cases is 20 (-c, --minCaseNumber).

• We have the option to choose whether to write out results for time-to-event = 0 (--saveT0).

• Example code:

$ Rscript a0_generator.r -i /path/to/test/cdc_first_test.tsv -m /path/to/test/disease_code_test.tsv --outfolder /path/to/outputfolder

More options available:

$ Rscript a0_generator.r -h
data.table doParallel    foreach   optparse 
      TRUE       TRUE       TRUE       TRUE 
Usage: Rscript a0_generator.r -i <inputFileName> -m <metaFileName> [options]

		 >> This the step 1 of EMR package. << 
	This R script will find the exposure population for all diesease pairs appearing in the input file that satisfy disease A -> disease B, and and second, it will find the matching non-exposed population for all diesease pairs with some criteria, such as the matching patient should have the same gender and race as a good match control. Outputs are CSV files with paired exposed and non-exposed subjects information. One folder named T0_include with CSV files with time-to-event = 0 could be produced if you turn on the --saveT0 flag. Those files will be used as inputs for step 2 of the package.


Options:
	-i CHARACTER, --infile=CHARACTER
		Input file name [required]. 
		Should be tab delimited with 6 columns in the order of patient_ID, Disease, Disease_Date ([%Y-%m-%d] or [%Y/%m/%d]), Age, Gender, Race. No header is needed. You could provide more information about the patient (additional columns), but only the measurement at disease A will be recorded

	-m CHARACTER, --metafile=CHARACTER
		Meta file for each disease name [required]. 
		First column is the disease ID used in the input file column Disease, second column is the disease name. All the other columns should be additional attribute of the disease, tab separated. Header is needed

	--outfolder=CHARACTER
		Intermediate files output folder, default is current directory

	--maxn=INTEGER
		Maximum number of subjects to be qualified as valid exposed cohort, default is 10000. If the total number of patients exceed this number, a subset of 5000 subjects will be randomly selected.

	--minn=INTEGER
		Minimum number of subjects to be qualified as valid exposed cohort, default is 100

	-c INTEGER, --minCaseNumber=INTEGER
		Minimum number of A->B cases to keep disease pair, default is 20

	--duration=INTEGER
		study duration (years), default is 5 years

	-y INTEGER, --year=INTEGER
		Age difference between exposed and non-exposed, default is 5 years

	-d INTEGER, --days=INTEGER
		Visit date difference between exposed and non-exposed, unit: days, default is 7 days

	--saveT0
		A flag to save the cohort tables with time-to-event = 0. The output CSVs will be saved to T0_include folder, default is false

	-p INTEGER, --processors=INTEGER
		Number of cores/CPUs to use, default is 8

	-h, --help
		Show this help message and exit

• Output: <DiseaseA>_<DiseaseB>.csv files.

• Example time table:

ID	type	time	event	V3	V4	V5	V6
P41812	0	350	0	9/4/11	68	F	White
P39443	0	770	0	11/7/10	52	M	White
P41112	0	0	0	3/4/10	70	M	White
P37186	0	0	0	12/24/16	67	F	White
P28958	0	146	0	10/5/14	59	F	White
P15618	0	1004	0	6/12/08	67	M	White
P14117	0	0	0	9/12/08	78	F	White
P24383	0	125	0	9/1/08	20	F	White
P00008	1	0	0	9/4/15	60	M	White
P00010	1	0	0	9/18/11	79	M	White
P00018	1	0	0	1/9/14	79	M	African American
P00028	1	805	0	6/5/10	55	M	White
P00040	1	222	0	1/4/10	85	F	White

Step 2: a1_analyzer.r

• Perform either Cox-PH regression or Random Forest survival analysis, taking age, race, gender as covariates (or any other confounding factors supplied by user), and final output is an adjacency matrix with all the adjusted significant P-values and survival curve graphs.

Cox-PH regression

• The default is to perform Cox-PH regression. Example code:

$ Rscript a1_analyzer.r -m /path/to/disease_code_test.tsv --inputfolder /path/to/all_csv_files/ --outputfolder /path/to/all_csv_files/outputs

• Example CoxPH.edge.csv file output (This won't match the result after you run the code):

from	to	coef	exp_coef	se_coef	z	Pr	N	HRtest-p	Pr.BH	from_name_long	to_name_long
14	23	1.337	3.809	0.137	9.786	<0.001	552	0.687	<0.001	Prostate Cancer	Glaucoma
23	14	1.056	2.875	0.138	7.631	<0.001	1568	0.942	<0.001	Glaucoma	Prostate Cancer
23	29	1.691	5.425	0.485	3.488	<0.001	1568	0.976	0.002	Glaucoma	Obesity
23	43	0.615	1.850	0.183	3.358	0.001	1568	0.677	0.002	Glaucoma	Acute Myeloid Leukemia
23	44	0.901	2.463	0.265	3.404	0.001	1568	0.506	0.002	Glaucoma	Vitiligo
23	509	1.651	5.214	0.173	9.561	<0.001	1568	0.279	<0.001	Glaucoma	Med:Progestins
23	63	0.769	2.158	0.239	3.212	0.001	1568	0.187	0.004	Glaucoma	Psoriasis
29	23	1.069	2.914	0.201	5.319	<0.001	244	0.212	<0.001	Obesity	Glaucoma
43	23	0.682	1.977	0.158	4.323	<0.001	350	0.069	<0.001	Acute Myeloid Leukemia	Glaucoma
44	509	0.550	1.732	0.248	2.213	0.027	424	0.473	0.057	Vitiligo	Med:Progestins
509	23	0.529	1.697	0.102	5.179	<0.001	1088	0.302	<0.001	Med:Progestins	Glaucoma

• Example survival curve:

In this test example, it shows the probability of getting Glaucoma across time between the population with and without Prostate Cancer. The strata =0 indicates the population without Prostate Cancer, while strata =1 indicates with Prostate Cancer. It suggests that people with Prostate Cancer develop Glaucoma faster than those who do not have Prostate Cancer.

• Example residual curve:

For the same Prostate Cancer to Glaucoma disease pair, the residuals lie closely to the diagonal line, meaning the data has a relative good fit for Cox-PH model.

• Example patient drop-off histogram:

It examines the drop-off subjects distribution for the two populations (having Prostate Cancer and not), and test whether they are similar. Given the P-value = 0.027, which is < 0.05, suggesting that those two distributions are statistically not similar to each other. Users should use caution when considering it to be a meaningful disease correlation.

Random Forest survival analysis

• To perform Random Forest survival analysis, run code:

Rscript a1_analyzer.r --method RF -m /path/to/disease_code_test.tsv --inputfolder /path/to/all_csv_files/ --outputfolder /path/to/all_csv_files/outputs

• Example RF.edge.csv file output (This won't match the result after you run the code):

from	to	Pr_wil	Pr_t	NonExposedMean	exposedMean	Pr_wil.BH	Pr_t.BH	from_name_long	to_name_long
14	23	<0.001	<0.001	1501.946	982.018	<0.001	<0.001	Prostate Cancer	Glaucoma
14	509	0.968	0.810	1482.072	1493.435	1.000	0.864	Prostate Cancer	Med:Progestins
23	14	<0.001	<0.001	1665.489	1466.806	<0.001	<0.001	Glaucoma	Prostate Cancer
23	29	<0.001	<0.001	1712.080	1681.140	<0.001	<0.001	Glaucoma	Obesity
23	43	<0.001	<0.001	1661.658	1587.812	<0.001	<0.001	Glaucoma	Acute Myeloid Leukemia
23	44	<0.001	0.001	1724.847	1680.445	<0.001	0.002	Glaucoma	Vitiligo
23	509	<0.001	<0.001	1759.704	1557.293	<0.001	<0.001	Glaucoma	Med:Progestins
23	59	0.001	0.581	1751.787	1752.578	0.002	0.661	Glaucoma	Chalazion
23	62	0.990	0.893	1694.242	1702.241	1.000	0.920	Glaucoma	Cirrhosis
23	63	<0.001	<0.001	1653.121	1607.370	<0.001	<0.001	Glaucoma	Psoriasis
23	67	0.172	0.467	1778.002	1771.577	0.254	0.615	Glaucoma	Sarcoidosis

• Example survival curve:

• More options:

$ Rscript a1_analyzer.r 

 randomForestSRC 2.5.0 
 
 Type rfsrc.news() to see new features, changes, and bug fixes. 
 

       survival randomForestSRC      data.table      doParallel         foreach 
           TRUE            TRUE            TRUE            TRUE            TRUE 
         OIsurv        optparse         ggplot2       ggfortify       gridExtra 
           TRUE            TRUE            TRUE            TRUE            TRUE 
Usage: Rscript a1_analyzer.r -i <inputFileName> -m <metaFileName> [options]

		 >> This is the step 2 of EMR package. << 
	This R script will perform either Cox-PH regression or random forest survival analysis on the valid files in result folder from step 1. 
		Outputs:
		 > CoxPH: an adjacency matrix with all the significant hazard ratios, hazard ratio test p-values, and survival curve and residual graphs.
		 > RF: Wilcoxon and T test p-values, mean time to event in exposed and non-exposed group, and survival curve graphs. 
		*Multiple test correction will be applied to the p-values in both methods.

Options:
	--inputfolder=CHARACTER
		Input folder name. 
		Should be a folder that contains all disease trajectories. Each file is named as NameA_NameB.csv. Default is current directory

	-m CHARACTER, --metafile=CHARACTER
		Meta file for each disease name [required]. 
		First column is the disease ID used in the input file column Disease, second column is the disease name. All the other columns should be additional attribute of the disease, tab separated. Header is needed

	--outputfolder=CHARACTER
		Survival analysis / random forest PNG output folder, default is the <inputfolder>

	--method=CHARACTER
		Survival Analysis method, choises are CoxPH, RF. The default is CoxPH

	-o CHARACTER, --outfile=CHARACTER
		Adjacency matrix output file name, default is <method>.edges.csv

	--duration=INTEGER
		study duration (years), default is 5 years

	-s DOUBLE, --sigcut=DOUBLE
		Significant P-value cutoff. Only p-values that are less than this cutoff will be considered as significant P-values, and kept in the adjacency matrix. Default is 0.05

	-e DOUBLE, --exp_coef=DOUBLE
		Exponentiated coefficients cutoff used in plotting survival curve. Default is 1.0

	-a CHARACTER, --adjust=CHARACTER
		Method of adjusting p-values, choices are holm, hochberg, hommel, bonferroni, BY, and fdr. The default is BH

	-n INTEGER, --ntree=INTEGER
		Number of trees to run random forest, default is 1000

	--pair
		A flag to control for matched subject in CoxPH. Default is false

	-p INTEGER, --processors=INTEGER
		Number of cores/CPUs to use, default is 8

	-h, --help
		Show this help message and exit

Step 3: a2_parse.py

• Parse the CoxPH adjacency matrix into a json object for webpage network display.

$ python a2_parse.py /path/to/CoxPH.edge.csv

• A screenshot of final network display. For interactive network display, go to http://cbi.lumc.edu/disease/.

Step 4: Copy results to web server directory

• Files: CoxPH.edge.csv, RF.edge.csv, all.edges.csv.js, and all PNG files should be in the same folder as the index.html.

cp /path/to/all_csv_files/outputs/* web_server

Version

• Version 1.6.3 Publication version
• Version 1.6 Major improvement on the speed

Authors

• Huaiying Lin. M.S., algorithm development, program coding and testing
• Dr. Xiang Gao, theoretical conception and algorithm development
• Dr. Qunfeng Dong, algorithm development
• Kashi Revanna, cytoscape visualization
• Petar Bajic, manuscript drafting and revision
• Michael Zhao, software testing
• Ruichen Rong, algorithm development, program coding and testing

Error report

Please report any errors or bugs to qunfengd@gmail.com.

It seems that "randomForestSRC 3.2.2" may cause problems for the following step:

Rscript a1_analyzer.r --method RF -m ./test/disease_code_test.tsv --inputfolder ./example --outputfolder ./example/output

Either try an older version of randomForestSRC, or just skip this step and analyze the results just based on the default Cox-PH regression.

License

GNU