EMeth: An EM algorithm for cell type decomposition based on DNA methylation data.

ABSTRACT: We introduce a new computational method named EMeth to estimate cell type proportions using DNA methylation data. EMeth is a reference-based method that requires cell type-specific DNA methylation data from relevant cell types. EMeth improves on the existing reference-based methods by detecting the CpGs whose DNA methylation are inconsistent with the deconvolution model and reducing their contributions to cell type decomposition. Another novel feature of EMeth is that it allows a cell type with known proportions but unknown reference and estimates its methylation. This is motivated by the case of studying methylation in tumor cells while bulk tumor samples include tumor cells as well as other cell types such as infiltrating immune cells, and tumor cell proportion can be estimated by copy n

SUBMITTER: Zhang H 

PROVIDER: S-EPMC7952399 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature