calculateDistMatOneModel

This function computes a similarity matrix by utilising 
a single linear model for differential expression analysis.

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 scRNA-Seq Integration and Evaluation

Christopher Yau

Ahmed Ahmed

calculateDistMatOneModel function

<dl><dt>matrix</dt>
<dd>A count matrix with rows representing genes or features and columns representing samples or cells.</dd>
<dt>metadata</dt>
<dd>A data frame containing metadata corresponding to the samples or cells. 
Each row should match a column in <code>matrix</code>.</dd>
<dt>verbose</dt>
<dd>Logical. If <code>TRUE</code>, the function displays progress messages 
and a progress bar. The default is <code>TRUE</code>.</dd>
<dt>method</dt>
<dd>A character string specifying the method for differential 
expression analysis. Options are "voom" or "trend", with "trend" as the default.</dd>
<dt>additional.variate</dt>
<dd>A character vector of additional variates to 
include in the linear model for regression.</dd></dl>

Arguments

Calculate Distance Matrix Using a Single Model — calculateDistMatOneModel

<dl>

<dt>matrix</dt>
<dd>A count matrix with rows representing genes or features and columns representing samples or cells.</dd>


<dt>metadata</dt>
<dd>A data frame containing metadata corresponding to the samples or cells. 
Each row should match a column in <code>matrix</code>.</dd>


<dt>verbose</dt>
<dd>Logical. If <code>TRUE</code>, the function displays progress messages 
and a progress bar. The default is <code>TRUE</code>.</dd>


<dt>method</dt>
<dd>A character string specifying the method for differential 
expression analysis. Options are "voom" or "trend", with "trend" as the default.</dd>


<dt>additional.variate</dt>
<dd>A character vector of additional variates to 
include in the linear model for regression.</dd>

</dl>

calculateDistMatOneModel: Calculate Distance Matrix Using a Single Model

Description

Usage

Value

Arguments

See Also