Deconvolution — deconvolute • methylDeconv

Deconvolution

Usage

deconvolute(
  methyl_set,
  method = deconvolution_methods,
  scale_results = FALSE,
  ...
)

Arguments

methyl_set: A minfi MethylSet
method: A string specifying the method. Supported methods are 'epidish', 'flowsorted', 'methylcc', 'methylresolver'
scale_results: Whether the deconvolution results should be rescaled. Negative values will be put to 0, and the estimates will be normalized to sum to 1. Defaults to FALSE.
...: Additional parameters, passed to the algorithm used. See individual method documentations for details.

Value

A matrix with the probabilities of each cell-type for each individual. Rows are individuals, columns are cell types.

Examples


ex_data <- minfiData::MsetEx
#> Setting options('download.file.method.GEOquery'='auto')
#> Setting options('GEOquery.inmemory.gpl'=FALSE)

result <- deconvolute(ex_data, method='epidish')
#> Warning: 12 NA values detected in your beta matrix. Replacing them with 0.5.
#> RPC was chosen as default for "mode"
#> blood was chosen as default for "reference"
#> Starting EpiDISH deconvolution with mode RPC ...