This package is designed to conduct "global analysis" of DNA methylation data, particularly from the Illumina 450k Infinium platform. Instead of examining the
effect of individual CpGs, the idea is to compare the overall profile or distribution of CpG measurements across individuals.
Briefly, each individual's methylation profile is
summarized by approximating the density of the methylation distribution OR the cumulative distribution function (CDF) of the methylation distribution using B-splines. The B-spline coefficients
are used to represent each individual's overall methylation distribution. To test for association between the overall distribution and a continuous or dichotomous variable
of interest, we apply the SKAT test (above) to the spline coefficients. A single p-value is generated.
Although the method is developed for DNA methylation data, it can be adapted to other types of data as well; however, the current software assumes that input values are
between 0 and 1 (corresponding to percent methylation).
This package depends on the fda and SKAT R packages.