make_deconv_pred_obs_data

Produces data with varied deconvolution performance metrics.

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

make_deconv_pred_obs_data function

<dl><dt>dat</dt>
<dd>data.frame with predictions as columns, each row should be a prediction for a given sample and given group/celltype</dd>
<dt>true_values_col</dt>
<dd>A string with the name of the column with the true values in `dat`. true values should be between 0 and 1.</dd>
<dt>predicted_cols</dt>
<dd>A vector of strings with the name of the columns with the predictions for different methods in `dat`. predictions should be between 0 and 1</dd>
<dt>sample_id_col</dt>
<dd>A string with the name of the column with the sample name or ID in `dat`.</dd>
<dt>group_col</dt>
<dd>A string with the name of the column containing the cell types or groups in `dat`. group col should be a factor, otherwise the function will make it a factor</dd></dl>

Arguments

Make tidy data for use in deconvolution plots — make_deconv_pred_obs_data

<dl>

<dt>dat</dt>
<dd>data.frame with predictions as columns, each row should be a prediction for a given sample and given group/celltype</dd>


<dt>true_values_col</dt>
<dd>A string with the name of the column with the true values in `dat`. true values should be between 0 and 1.</dd>


<dt>predicted_cols</dt>
<dd>A vector of strings with the name of the columns with the predictions for different methods in `dat`. predictions should be between 0 and 1</dd>


<dt>sample_id_col</dt>
<dd>A string with the name of the column with the sample name or ID in `dat`.</dd>


<dt>group_col</dt>
<dd>A string with the name of the column containing the cell types or groups in `dat`. group col should be a factor, otherwise the function will make it a factor</dd>

</dl>

make_deconv_pred_obs_data: Make tidy data for use in deconvolution plots

Description

Usage

Value

Arguments