Genome-wide genetic heterogeneity discovery with categorical covariates (FastCMH)

Enlarged view: Cover of the Bioinformatics journal

Felipe Llinares-Lopez, Laetitia Papaxanthos, Dean Bodenham, Damian Roqueiro, COPDGene Investigators and Karsten Borgwardt

Genome-wide genetic heterogeneity discovery with categorical covariates

Summary

We present an algorithm to discover genomic regions of contiguous SNPs that are associated to a phenotype of interest under a model of genetic heterogeneity. The algorithm can search any contiguous set of SNPs in the genome while still properly correcting for mutiple testing and accounting for confounding factors.

Code

A beta version of the FastCMH algorithm is available in our GitHub repository external pagehere.

R package

The R package ‘fastcmh’ can be installed from CRAN external pagehere. It requires R version 3.3.0 or above.

Then, in an R session, first install the packages ‘bindata’ and ‘Rcpp’ using the commands:

> install.packages(“bindata”)

> install.packages(“Rcpp”)

Next, install 'fastcmh':

> install.packages(“fastcmh”)

For information on how to use ‘fastcmh’, please refer to the Supplementary Material of the paper or look at the external pagedocumentation for FastCMH in CRAN.

Publication