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]