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Detection of statistically significant combinations of SNPs in association mapping
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README.md

CASMAP

Combinatorial ASsociation MAPping

A repository with the source code of the CASMAP package (Application Note submission).

Contents:

Downloading the repository

Clone the repository with the git command

git clone https://github.com/BorgwardtLab/CASMAP.git

The location of the downloaded repository will be referred to as root folder.

Alternatively, download the repository as a ZIP file and decompress in your local computer.

Installation and compilation

Firstly, all dependencies must be installed (R, Python, various packages - see detailed instructions below). After that, installing CASMAP is simple.

Step 1: Obtaining the C++ compiler

The current version uses the GCC 6 compiler (gcc-6) in the Makefiles. For Linux (Ubuntu), GCC 6 can be installed using the following commands:

sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get update
sudo apt-get install gcc-6 g++-6

For Mac OSX, install GCC 6 with the following commands:

brew update
brew install gcc@6

Step 2: Compiling the code base and R/Python packages

The commands below apply to both Linux and Mac OSX.

Change directory to the root folder. There, simply run:

Compilation of core functions

make

Compilation of the R wrapper

From the root folder change directory to the subdirectory r_wrapper:

cd r_wrapper

Run the command:

make package

Troubleshooting: If the previous command does not work, then run:

Rscript -e "devtools::build()"

which will then create the R package .tar.gz file.

Compilation of the Python wrapper

From the root folder change directory to the subdirectory cython_wrapper:

cd cython_wrapper

Run the command:

make

Troubleshooting: If the previous command fails with make: *** [wrapper] Error 1, then run:

export CC=gcc-6
make

which will make sure that the compilation is done with a newer version of the gcc compiler.

Uninstall

To remove the compiled files (perhaps before recompiling), in the root folder run:

make clean

Step 3: Installing the R package

Follow the steps described in the README.md file under the subdirectory r_wrapper.

Step 4: Installing the Python package

Follow the steps described in the README.md file under the subdirectory cython_wrapper.

Troubleshooting

On Ubuntu 16.04, make sure the following packages are installed:

  • libxml2-dev (needed for R's devtools)
  • curl (needed for R's devtools)
  • libcurl4-openssl-dev (needed for R's devtools)
  • libssl-dev (needed for R's devtools)
  • ipython (for convenience)
  • cython (for the python wrapper)
  • python-pip (installs setuptools, which is needed for the python wrapper)

These can be installed with the following commands.

sudo apt-get install libxml2-dev
sudo apt-get install curl
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libssl-dev
sudo apt install python-pip
sudo apt install ipython
sudo apt install cython

The R wrapper

In order to have use the R wrapper, the R language needs to be installed. Moreover, a few packages need to be installed, in particular devtools. In R:

install.packages("devtools", dependencies=T)

Note that this will take a long time! If a few dependencies are not successfully installed, just make sure that the following works in R:

library(devtools)

Follow the steps described in the README.md file under the subdirectory r_wrapper.

The Python wrapper

Similarly, for the Python wrapper to work, we need Python to be installed. We also need cython and pip to be installed. One way to do this is to follow the instructions on this page.

Installing sphinx

If one uses

make clean

in the cython folder, the message that sphinx-build is missing might appear. To install it in Ubuntu:

sudo apt-get install python-sphinx

To install it in OSX:

sudo pip install --upgrade pip
pip install sphinx --user

Follow the steps described in the README.md file under the subdirectory cython_wrapper.

Examples

The repository includes examples that illustrate how to use CASMAP to carry out region-based association studies and higher-order epistasis search.

The folder examples/data provides a real-world dataset from the plant model organism A. thaliana, downloaded from the easyGWAS online resource.

  • examples/data/region_based/avrB contains: 1) X.dat, the genotypes of 87 samples measured at 214,032 homozygous SNPs; 2) Y.dat, the binary phenotype avrB for each of the 87 samples, 3) C.dat, a categorical covariate to account for population structure; and 4) plink.map, a list with the locations of all SNPs in the genome of A. thaliana.
  • examples/data/higher_order_epistasis/avrB is analogous, but file X.dat in this folder consists of a subset of 650 SNPs in Chromosome 1.

The folder examples/code contains Python/R Jupyter notebooks which show how CASMAP can be used to analyze these datasets.

  • run_region_based.ipynb (Python) and run_region_based.Rmd (R) describe the region-based association study example.
  • run_higher_order_epistasis.ipynb (Python) and run_higher_order_epistasis.Rmd (R) describe the higher-order epistasis search example.

The notebooks are heavily commented, aiming to provide a comprehensive, guided explanation of how to use CASMAP. For additional details about these examples, we refer the user to the Supplementary Material of the Application Note.

Additional examples, as well as slides describing the theory behind the methods included in CASMAP, can be found as part of the material of the following tutorial, which took place in ISMB 2018.

Installing the R package from CRAN

CASMAP is also available as an R package on the The Comprehensive R Archive Network (CRAN), and can be installed in an R session using:

install.packages("CASMAP")
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