CpGFilter (version 1.0)

CpGFilter-package: CpG filtering method based on linear mixed effects model.

Description

Filter CpGs based on Intra-class Correlation Coefficients (ICCs). ICCs are calculated by fitting linear mixed effects models to all samples including the un-replicated samples. Including the large number of un-replicated samples improves ICC estimates dramatically. The method accommodates any replicate design.

Details

Package:	CpGFilter
Type:	Package
Version:	1.0
Date:	2014-10-31
License:	GPL-2

References

CpGFilter:Model-based CpG probe filtering with replicates for epigenome-wide association studies (2014). Submitted.

Examples

# NOT RUN {
require(CpGFilter)
rep.design <- c(1:900, 901:910, 901:910, 911:915, 911:915, 911:915, 911:915)
rho <- CpGFilterICC(matrix(rnorm(940*10000), 10000, 940), rep.design, logit=FALSE)
# }