Seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data.

ABSTRACT:

Motivation

One of the main goals of large scale methylation studies is to detect differentially methylated loci. One way is to approach this problem sitewise, i.e. to find differentially methylated positions (DMPs). However, it has been shown that methylation is regulated in longer genomic regions. So it is more desirable to identify differentially methylated regions (DMRs) instead of DMPs. The new high coverage arrays, like Illuminas 450k platform, make it possible at a reasonable cost. Few tools exist for DMR identification from this type of data, but there is no standard approach.

Results

We propose a novel method for DMR identification that detects the region boundaries according to the minimum description length (MDL) principle, essentially solving the problem of model

SUBMITTER: Kolde R 

PROVIDER: S-EPMC5013909 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature