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

View source: R/estimate-cell-counts.r

meffil.estimate.cell.countsR Documentation

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.