residuals.deconv

Extracts residuals from a deconvolution model. As the model uses a reduced
signature gene set for deconvolution, in order to extract residuals for all
genes, these need to recalculated by supplying the bulk count matrix <code>test</code>.

Deconvolution of bulk RNA-Sequencing data into proportions of cells based on a reference single-cell RNA-Sequencing dataset using high-dimensional geometric methodology.

Myles Lewis

cellGeometry

Geometric Single Cell Deconvolution

Rachel Lau

residuals.deconv function

<dl><dt>object</dt>
<dd>a 'deconv' class object</dd>
<dt>test</dt>
<dd>bulk gene expression matrix assumed to be in raw counts</dd>
<dt>arith_mean</dt>
<dd>logical, whether to use arithmetic mean as gene signature</dd>
<dt>use_filter</dt>
<dd>logical, whether to use denoised signature matrix</dd>
<dt>...</dt>
<dd>retained for class compatibility</dd></dl>

Arguments

Extract Deconvolution Residuals — residuals.deconv

<dl>

<dt>object</dt>
<dd>a 'deconv' class object</dd>


<dt>test</dt>
<dd>bulk gene expression matrix assumed to be in raw counts</dd>


<dt>arith_mean</dt>
<dd>logical, whether to use arithmetic mean as gene signature</dd>


<dt>use_filter</dt>
<dd>logical, whether to use denoised signature matrix</dd>


<dt>...</dt>
<dd>retained for class compatibility</dd>

</dl>

residuals.deconv: Extract Deconvolution Residuals

Description

Usage

Value

Arguments