calculateDistMatOneModel

This function is called by `getDistMat`.

A workflow of (a) meta-clustering based on
inter-group similarity measures and (b) a ground-truth-free test metric to
assess the biological correctness of integration in real datasets. See Hu Z,
Ahmed A, Yau C (2021) <doi:10.1101/2021.03.29.437525> for
more details.

Zhiyuan Hu

CIDER

Meta-Clustering for Single-Cell Data Integration and Evaluation

Christopher Yau

calculateDistMatOneModel function

<dl><dt>matrix</dt>
<dd>The count matrix. Rows are genes/features and columns are
samples/cells.</dd>
<dt>metadata</dt>
<dd>Data frame. Its rows should correspond to
columns of the `matrix` input.</dd>
<dt>verbose</dt>
<dd>Print the message and progress bar (default: TRUE)</dd>
<dt>method</dt>
<dd>Methods for DE analysis. Options: "voom" or "trend" (default)</dd>
<dt>additional.variate</dt>
<dd>additional variate to include into the linear
model to regress out</dd></dl>

Arguments

Author

Calculate distance matrix with in one model — calculateDistMatOneModel

<dl>

<dt>matrix</dt>
<dd>The count matrix. Rows are genes/features and columns are
samples/cells.</dd>


<dt>metadata</dt>
<dd>Data frame. Its rows should correspond to
columns of the `matrix` input.</dd>


<dt>verbose</dt>
<dd>Print the message and progress bar (default: TRUE)</dd>


<dt>method</dt>
<dd>Methods for DE analysis. Options: "voom" or "trend" (default)</dd>


<dt>additional.variate</dt>
<dd>additional variate to include into the linear
model to regress out</dd>

</dl>

calculateDistMatOneModel: Calculate distance matrix with in one model

Description

Usage

Value

Arguments

Author

See Also