Hands-on session: Package CASMAP

1. Package overview

The CASMAP package (Combinatorial ASsociation MAPping) combines three different methods and publicly available tools into on software tool.

FAIS: F. Llinares-López et al. (2015) Bioinformatics, 31 (12): i240-i249)
FACS: L. Papaxanthos et al. (2016 ) Advances in Neural Information Processing Systems 29 (NIPS 2016), 2271-2279
FastCMH: F. Llinares-López et al. (2017) Bioinformatics, 33 (12): 1820-1828)

1.1 Repository of methods and publications

Here you can find links to all our publications on the topic of significant pattern mining.

1.2 Functionality

The package was tailored to process genomic data, but it also allows for custom input files to conduct other more generic analises. A key feature of this package is its ability to correct for known confounders in the data, e.g. population stratification in GWAS.

Interval search: also “Region-based genome-wide association studies”, considers sets of features that are adjacent to each other. In the case of SNPs, it will consider genomic regions marked by a start and end SNP.
Combinatorial search: also “High-order Epistasis” (the FACS tool), considers any order combination of features.

Region-based GWAS

Note: Figure extracted from Felipe’s presentation (Module I)

High-order epistasis

Note: Figure extracted from Felipe’s presentation (Module I)

2. Package installation

The CASMAP package is available for R (ver. 3.4+) and Python (ver. 2.7+ or 3).

2.1 For R

The package is available on CRAN
Source code and step-by-step installation instructions can be found in our GitHub repository

2.2 For Python

Currently, installation is only available from source. You can find all the details in our GitHub repository

3. Virtual machine

In case of problems with the installation steps, we have created a virtual machine (VM) with Ubuntu 14.04. The VM has the packages we will use in the hands-on sessions pre-installed. See more details here.

3. Program for the rest of the session

Today we will discuss three different examples on how to use CASMAP.

Example 1: Combinatorial motif binding
Example 2: Region-based GWAS in Arabidopsis thaliana
Example 3: Higher-order epistasis in Arabidopsis thaliana