meffilEstimateCellCountsFromBetas {methylclock} | R Documentation |
Estimate cell type ratios from methylation profiles of purified cell populations (Infinium HumanMethylation450 BeadChip).
meffilEstimateCellCountsFromBetas(beta, cellTypeReference, verbose = FALSE)
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 |
verbose |
If |
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
A matrix of cell count estimates.
Results should be nearly identical to estimateCellCounts() function in minfi package
betas
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)