run_deconvolution: Perform deconvolution on a new set of samples, based on the...

In CimpleG: A Method to Identify Single CpG Sites for Classification and Deconvolution

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

Description

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'.

Value

a data.table with the deconvolution results

CimpleG documentation built on Dec. 7, 2025, 1:07 a.m.