Probe Lasso: a novel method to rope in differentially methylated regions with 450K DNA methylation data.

ABSTRACT: The speed and resolution at which we can scour the genome for DNA methylation changes has improved immeasurably in the last 10years and the advent of the Illumina 450K BeadChip has made epigenome-wide association studies (EWAS) a reality. The resulting datasets are conveniently formatted to allow easy alignment of significant hits to genes and genetic features, however; methods that parse significant hits into discreet differentially methylated regions (DMRs) remain a challenge to implement. In this paper we present details of a novel DMR caller, the Probe Lasso: a flexible window based approach that gathers neighbouring significant-signals to define clear DMR boundaries for subsequent in-depth analysis. The method is implemented in the R package ChAMP (Morris et al., 2014) and returns set

SUBMITTER: Butcher LM 

PROVIDER: S-EPMC4304833 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature