Genome-wide DNA methylation sites screening by use of training and testing samples.

Description

A screening process to filter out non-informative DNA methylation sites by applying (ordinary or robust) linear regressions to training data, and the results are further examined using testing samples. Surrogate variables are included to account for unknown factors.

Details

This package utilizes training and testing samples to filter out uninformative DNA methylation sites. Surrogate variables (SVs) of DNA methylation are included in the filtering process to explain unknown factor effects.

Author(s)

Meredith Ray, Xin Tong, Hongmei Zhang

Maintainer: Meredith Ray <mere2110@yahoo.com>

References

Meredith Ray, Xin Tong, Hongmei Zhang, and Wilfred Karmaus. (2014) "DNA methylation sites screening with surrogate variables", unpublished manuscript.

Leek JT and Storey JD. (2007) "Capturing heterogeneity in gene expression studies by ‘Surrogate Variable Analysis’." PLoS Genetics, 3: e161.

See Also

sva

Results