Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach.

ABSTRACT:

Motivation

It is a common practice in epigenetics research to profile DNA methylation on tissue samples, which is usually a mixture of different cell types. To properly account for the mixture, estimating cell compositions has been recognized as an important first step. Many methods were developed for quantifying cell compositions from DNA methylation data, but they mostly have limited applications due to lack of reference or prior information.

Results

We develop Tsisal, a novel complete deconvolution method which accurately estimate cell compositions from DNA methylation data without any prior knowledge of cell types or their proportions. Tsisal is a full pipeline to estimate number of cell types, cell compositions and identify cell-type-specific CpG sites. It can also assi

SUBMITTER: Zhang W 

PROVIDER: S-EPMC8150138 | biostudies-literature | 2021 May

REPOSITORIES: biostudies-literature