deconvolution_epidish

DNA methylation signatures are usually based on multivariate
approaches that require hundreds of sites for predictions. 'CimpleG'
is a method for the detection of small CpG methylation signatures used
for cell-type classification and deconvolution. 'CimpleG' is time
efficient and performs as well as top performing methods for cell-type
classification of blood cells and other somatic cells, while basing
its prediction on a single DNA methylation site per cell type (but
users can also select more sites if they so wish). Users can train
cell type classifiers ('CimpleG' based, and others) and directly apply
these in a deconvolution of cell mixes context. Altogether, 'CimpleG'
provides a complete computational framework for the delineation of
DNAm signatures and cellular deconvolution. For more details see Maié
et al. (2023) <doi:10.1186/s13059-023-03000-0>.

Tiago F.V. Maié

CimpleG

A Method to Identify Single CpG Sites for Classification and
Deconvolution

deconvolution_epidish function

<dl><dt>ref_mat</dt>
<dd>Reference matrix.</dd>
<dt>new_data</dt>
<dd>New data matrix.</dd>
<dt>epidish_method</dt>
<dd>One of `CBS` (Cibersort), `RPC` (Robust Partial Correlations), `CP` (Constrained Projection).
Default is `CBS`. See `EpiDISH` documentation for more information.</dd>
<dt>epidish_nuv</dt>
<dd>A vector of candidate values used for svm. Only used when epidish_method is set to `CBS`.
See `EpiDISH` documentation for more information.</dd>
<dt>epidish_maxit</dt>
<dd>Integer with the number of max iterations for IWLS (Iterative Weighted Least Squares).
Only used when epidish_method is set to `RPC`.</dd></dl>

Arguments

EpiDISH deconvolution — deconvolution_epidish

<dl>

<dt>ref_mat</dt>
<dd>Reference matrix.</dd>


<dt>new_data</dt>
<dd>New data matrix.</dd>


<dt>epidish_method</dt>
<dd>One of `CBS` (Cibersort), `RPC` (Robust Partial Correlations), `CP` (Constrained Projection).
Default is `CBS`. See `EpiDISH` documentation for more information.</dd>


<dt>epidish_nuv</dt>
<dd>A vector of candidate values used for svm. Only used when epidish_method is set to `CBS`.
See `EpiDISH` documentation for more information.</dd>


<dt>epidish_maxit</dt>
<dd>Integer with the number of max iterations for IWLS (Iterative Weighted Least Squares).
Only used when epidish_method is set to `RPC`.</dd>

</dl>

deconvolution_epidish: EpiDISH deconvolution

Description

Usage

Arguments