estimate_props_qp: Estimate cell type proportions

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

Estimate cell type proportions

Description

This function will estimate the proportions of constituent cell types in each input sample, given methylation profiles of complex tissue samples and methylation profiles of constituent cell types.

Usage

estimate_props_qp(meth_bulk_samples, cell_type_specific_meth)

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_specific_meth	Matrix of methylation profiles of constituent cell types. Columns correspond to different cell types and rows correspond to different loci/probes.

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 methylation profiles of constituent cell types this function estimates cell type proportions in each sample by solving constrained least squares problems through quadratic programming. The constraints are that the proportions of constituent cell types are numbers in the 0,1 interval and that the proportions of all cell types in each sample sum up to one.

Value

Matrix with estimated proportions of constituent cell types in each sample.

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