MATLAB source code to accompany the PLoS Genetics paper, "Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease".
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README.md

README.md

bmapathway

This repository contains MATLAB source code and scripts for integrated analysis of genetic variants and pathways in genome-wide data sets for seven complex diseases: bipolar disorder (BD), coronary artery disease (CAD), Crohn's disease (CD), hypertension (HT), rheumatoid arthritis (RA), type 1 diabetes (T1D) and type 2 diabetes (T2D). These data sets are from the Wellcome Trust Case-Control Consortium (WTCCC) studies (the initial results of these studies were published in Nature in 2007).

Running the MATLAB scripts in the MATLAB/analysis folder should reproduce the results of our PLoS Genetics paper, "Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease." For more details on the methods used, please consult the PLoS Genetics paper.

This repository also contains MATLAB code implementing statistical procedures to (1) interrogate support for enrichment of disease associations in genome-wide data; and (2) map genetic variants associated with disease risk. The mapping prioritizes genetic variants assigned to enriched gene sets, in an attempt to enhance discovery of genes underlying complex diseases. Our statistical procedures are based on fitting multi-marker models of disease to the data. We use Bayesian model averaging (BMA) in large-scale multivariate regression to quantify support for enrichment models, and to infer disease associations conditioned on these models.

License

Copyright (c) 2013, Peter Carbonetto.

The bmapathway project repository by Peter Carbonetto is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The bmapathway project repository is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See LICENSE for more details.

Note about the data

The data used in the analyses are stored in the data folder: pathway.mat stores gene sets retrieved from online pathway databases, such as KEGG and Reactome; gene.mat stores information about how genes are annotated to the human genome (note that we use version 17, or NCBI Build 35, of the Human Genome Assembly because the data from the WTCCC disease studies are also based on this assembly). However, we cannot make the full genotype data available due to privacy considerations; even if we were allowed to release these data, space restrictions on github would prevent us from storing these files in the repository. Instead, we provide "representative" files containing information about the genetic markers (these markers are single nucleotide polymorphisms, or SNPs), except that the n x p genotype matrix (where n is the number of samples, and p is the number of SNPs) is replaced by an n x p sparse matrix, in which only a few columns of this matrix have nonzero entries. The nonzero entries are minor allele counts at the SNPs, in which the rows have been permuted to preserve privacy. Thus, only the minor allele frequency of each of these SNPs is preserved in the data we have made available. For example, in the Crohn's disease data set, cd.mat, the 4686 x 442,001 matrix of genotypes is replaced by a sparse matrix of the same size, in which we have provided permuted genotypes for only 10,000 of the 442,001 SNPs.

Overview of the MATLAB code

The MATLAB folder is organized into several subfolders. All the MATLAB code (.m files) is found within these subfolders. There are many files in these subfolders defining various MATLAB functions used for our statistical analysis procedures. Here we point out the most important folders and files, and explain when they might be useful.

  • The analysis folder contains the main scripts that run all steps of the integrated analysis for the seven diseases, as well as a few other functions for loading structures used in the analysis. All these scripts have several stages to the analysis. To complete the analysis, you will need to generate the results of each of these stages, in order. For example, the analysis of the Crohn's disease data set takes 11 separate steps. This includes computation of posterior quantities from the multi-marker model without pathways (Stages A and B), computation of Bayes factors for candidate gene sets retrieved from online pathway databases (Stages C and D), computation of Bayes factors for combinations of enriched pathways (Stages E through J), and finally computation of some posterior quantities conditioned on enrichment models with the largest Bayes factors (Stage K). All of these steps are implemented in the MATLAB script cdpath.m.

  • The results folder contains several functions and a script, compileresults.m, that compiles results from the analysis for all seven diseases, and generates tables and graphs for the PLoS Genetics paper.

  • MATLAB functions implementing our main statistical procedures are stored in the multisnp folder. Function multisnpbinhyper runs the full variational inference procedure for Bayesian variable selection in logistic regression. It fits the multi-marker disease model to the data under the null hypothesis that no pathways are enriched for disease associations. Function bayesfactorbin computes the Bayes factor for a specified pathway annotation. It does so by fitting the multi-marker disease model to the data under the hypothesis that markers assigned to the pathway are enriched for diseases associations. Function varpathbin computes Bayes factors for a list of candidate pathways. We have implemented variants to each of these procedures, multisnpbinhyper2, bayesfactorbin2 and varpathbin2. These variants are used for the modified analysis of the rheumatoid arthritis and type 1 diabetes data sets. These modifications are needed to account for the outsized contributions of the major histocompatibility complex (MHC) to disease risk.

  • The data folder contains several functions and a script, getwtcccdata.m, for acquiring and processing the genotype data, and for storing it in a convenient format for subsequent analysis steps. The genotype data was originally stored in files for use by the program BIMBAM, but these files are not available here because they are large, and would infringe on privacy of study participants. Therefore, the functions in this folder are unlikely to be useful unless you have access to the BIMBAM files, or to the files from the original WTCCC study.

  • The genes folder contains multiple functions and a script, getgenedata.m, for reading gene annotation files into MATLAB. The MATLAB data file gene_35.1.mat was generated by this script. This file contains information about where genes are annotated to the human reference sequence.

  • The pathways folder contains a number of functions and a script, getpathwaydata.m, for reading pathway gene sets from various pathway databases (Reactome, KEGG, PANTHER, etc) into MATLAB. The MATLAB data file pathway.mat was generated with this script. This file contains gene set annotations for all 3160 candidate pathways included in our analyses.

  • The mhc folder contains a couple functions that define SNP annotations for the MHC and "extended" MHC.

  • The stats folder contains a few functions that output various statistical quantities used in our analyses.

  • Finally, the misc folder contains several miscellaneous subroutines used by other functions.

Downloading and using the MATLAB code

As we explained above, it is not possible to reproduce our results from this repository alone; you must have access to the SNP data from the WTCCC studies. However, the MATLAB source code in this repository may still be useful to you if you would like to attempt an integrated analysis of pathways and genetic variants for your own study.

To use the code, the first step is to copy the files to your computer. This can be done either by downloading and unpacking the ZIP file, or by cloning the repository from the command line (assuming you have git installed on your computer):

git clone git@github.com:pcarbo/bmapathway.git

To call the functions in MATLAB, you will probably need to add the subdirectories to your path using the ADDPATH command in MATLAB.

You will also need to download the MATLAB functions implemented in the varbvs repository, and follow the instructions in that repository to build the MEX files.

We ran all the code in this repository in MATLAB 7.10 (R2010a) on Linux machines. We also ran some of the code in a more recent MATLAB release, 7.14 (R2012a). We cannot guarantee that these functions will run correctly in the most current versions of MATLAB, or with operating systems other than Linux (though we have no reason at this point to expect that the code will not run successfully).

Finally, we warn that running these MATLAB scripts can be extremely memory intensive for the sorts of genome-wide data sets we investigated. It may require a computer with more memory than is available in most conventional desktop computers; some of the steps of our analysis required as much as 20 Gb of RAM.

Credits

All MATLAB source code contained in this repository was developed by:
Peter Carbonetto
Dept. of Human Genetics
University of Chicago
August 2013