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
Bioinformatics 2017, 33 (12): 1820-1828. (Online)

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

@article{Llinares-Lopes-2017-Bioinformatics,
author = {Llinares-López, Felipe and Papaxanthos, Laetitia and Bodenham, Dean and Roqueiro, Damian and {COPDGene Investigators} and Borgwardt, Karsten},
title = {Genome-wide genetic heterogeneity discovery with categorical covariates},
journal = {Bioinformatics},
volume = {33},
number = {12},
pages = {1820},
year = {2017},
doi = {10.1093/bioinformatics/btx071},
URL = {http://dx.doi.org/10.1093/bioinformatics/btx071}
}

Contact and for questions regarding usage or reporting bugs.

 
 
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Sat Jun 24 00:48:52 CEST 2017
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