meffilEstimateCellCountsFromBetas {methylclock}R Documentation

Estimate cell counts for a beta matrix from a reference

Description

Estimate cell type ratios from methylation profiles of purified cell populations (Infinium HumanMethylation450 BeadChip).

Usage

meffilEstimateCellCountsFromBetas(beta, cellTypeReference, verbose = FALSE)

Arguments

beta

Matrix of Illumina 450K methylation levels (rows = CpG sites, columns = subjects).

cellTypeReference

Character string name of the cell type reference to use for estimating cell counts. See meffilListCellTypeReferences() for a list of available references. New references can be created using

verbose

If TRUE, then status messages are printed during execution (Default: FALSE).

Details

ORIGINAL AUTHOR: Matthew Suderman The original meffil.list.cellTypeReferences and get.cellTypeReference function from meffil v1.0.0 downloaded from githug : https://github.com/perishky/meffil

Value

A matrix of cell count estimates.

Results should be nearly identical to estimateCellCounts() function in minfi package

betas

Examples


cell.count.reference <- "andrews and bakulski cord blood"
TestDataset <- get_TestDataset()
cpgs <- t(as.matrix(TestDataset[, -1]))
colnames(cpgs) <- TestDataset$CpGName
meffilEstimateCellCountsFromBetas(t(cpgs), cell.count.reference)

[Package methylclock version 1.0.1 Index]