Perform deconvolution on a new set of samples, based on the CimpleG models trained

Perform deconvolution on a new set of samples, based on the CimpleG models trained

Usage

run_deconvolution(
  cpg_obj = NULL,
  new_data = NULL,
  ref_mat = NULL,
  deconvolution_method = c("NNLS", "EpiDISH", "NMF"),
  ...
)

Arguments

cpg_obj

A CimpleG object. When creating/training CimpleG the parameter `deconvolution_reference` should be set to `TRUE`.

new_data

Matrix or data.frame that should have the samples you want to perform deconvolution on. Samples should be in rows and probes/CpGs in columns.

ref_mat

If the CimpleG object does not have the reference matrix, you can provide it here instead. See `make_deconv_ref_matrix`

deconvolution_method

Deconvolution method to be used. One of #TODO

...

Extra parameters only used when deconvolution_method is set to `NMF`. The most relevant parameter are probably `method` and `beta`.