Our R package Mega2R is now available in CRAN

[Dan Weeks]

Announcement:  

Mega2R will let you easily bring your genetic data into R, as well as facilitates looping over genes to carry out gene-based association tests with other R packages.

The Mega2R R package now makes it easy to load SQLite3 Mega2 databases directly into R as data frames. In addition, we have developed C++ functions for R to decompress needed subsets of the genotype data, on the fly, in a memory efficient manner. 

We have also created several more functions that illustrate how to use the Mega2R data frames as well as perform useful tasks: these permit one to run the pedgene package to carry out gene-based association tests on family data using selected marker subsets, to run the SKAT package to carry out gene-based association tests using selected marker subsets, to output the Mega2R data as a VCF file and related files (for phenotype and family data), and to convert the data frames into GenABEL  R gwaa.data-class objects. The Mega2R package enhances GenABEL since it supports additional input data formats (such as PLINK, VCF, and IMPUTE2) not currently supported by GenABEL. 

Mega2R is available here: https://CRAN.R-project.org/package=Mega2R. 

An nice HTML version of the vignette is available here: https://watson.hgen.pitt.edu/mega2/mega2r/