meffil.estimate.cell.counts: Estimate cell counts from a reference

In perishky/meffil: Efficient algorithms for DNA methylation

Estimate cell counts from a reference

Description

Estimate cell type ratios from methylation profiles of purified cell populations (Infinium HumanMethylation450 BeadChip) using the the Houseman algorithm (PMID 22568884).

Usage

meffil.estimate.cell.counts(qc.object, cell.type.reference, verbose = T)

Arguments

cell.type.reference	Character string name of the cell type reference to use for estimating cell counts. See meffil.list.cell.type.references() for a list of available references. New references can be created using meffil.add.cell.type.reference().
verbose	If TRUE, then status messages are printed during execution (Default: FALSE).
object	An object created by meffil.create.qc.object().

Value

A list:

• counts Cell count estimates.

• beta Normalized methylation levels of sites used to differentiate

• reference Name of the cell type reference used. between reference cell types.

Results should be nearly identical to estimateCellCounts().

perishky/meffil documentation built on June 9, 2024, 5:59 p.m.