estimate_meth_qp: Estimate cell type specific methylation

In bozdaglab/CTDPathSim2.0: Computing multi-omics driven similarity scores between patient tumor samples and cell lines for personalized medicine

Estimate cell type specific methylation

Description

Given methylation profiles of complex tissue samples and propotions of contituent cell types in each sample, estimate_meth_qp will estimate average methylation profiles of constituent cell types across the set of input samples.

Usage

estimate_meth_qp(meth_bulk_samples, cell_type_props)

Arguments

meth_bulk_samples	Matrix of methylation profiles of bulk complex tissue samples. Columns correspond to different samples and rows correspond to different loci/probes.
cell_type_props	Matrix of proportions of constituent cell types. Columns correspond to different cell types and rows correspond to different bulk tissue samples.

Details

EDec assumes that the methylation profiles of complex tissue samples correspond to the linear combination of cell type proportions and methylation profiles of each cell type. Given the methylation profiles of a set of complex tissue samples and the proportions of constituent cell types in each sample, this function estimates average methylation profiles of constituent cell types by solving constrained least squares problems through quadratic programming. The constraint is that the methylation profiles of constituent cell types are numbers in the 0,1 interval.

Value

Matrix with estimated average methylation profiles of constituent cell types.

bozdaglab/CTDPathSim2.0 documentation built on April 14, 2022, 12:39 a.m.