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

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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 here.

R package

The R package ‘fastcmh’ can be installed from CRAN here. 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 documentation for FastCMH in CRAN.

Reference

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Felipe Llinares-Lopez*, Laetitia Papaxanthos*, Dean Bodenham, Damian Roqueiro, COPDGene Investigators and Karsten Borgwardt (*=equal contributions)
Genome-wide genetic heterogeneity discovery with categorical covariates
Accepted at Bioinformatics 2017. (Online)

Further information and the code can be found on the project page.

To appear after publication.

Contact and for questions regarding usage or reporting bugs.

 
 
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Thu Apr 27 23:15:04 CEST 2017
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