estimateProb

This function computes the empirical probability that two sets of cells from 
distinct batches belong to the same population, based on the output of <code>getIDEr</code>.

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

estimateProb function

<dl><dt>seu</dt>
<dd>A Seurat object.</dd>
<dt>ider</dt>
<dd>A list returned by the <code>getIDEr</code> function.</dd>
<dt>batch.var</dt>
<dd>Character string specifying the metadata column that contains 
batch information. Default is "Batch".</dd>
<dt>n_size</dt>
<dd>Numeric value indicating the number of cells per group used to 
compute the similarity. Default is 40.</dd>
<dt>n.perm</dt>
<dd>Numeric value specifying the number of permutations to perform.</dd>
<dt>verbose</dt>
<dd>Logical. If <code>TRUE</code>, progress messages are printed. 
Default is <code>FALSE</code>.</dd></dl>

Arguments

Estimate the Empirical Probability of Whether Two Set of Cells
from Distinct Batches Belong to the Same Population — estimateProb

<dl>

<dt>seu</dt>
<dd>A Seurat object.</dd>


<dt>ider</dt>
<dd>A list returned by the <code>getIDEr</code> function.</dd>


<dt>batch.var</dt>
<dd>Character string specifying the metadata column that contains 
batch information. Default is "Batch".</dd>


<dt>n_size</dt>
<dd>Numeric value indicating the number of cells per group used to 
compute the similarity. Default is 40.</dd>


<dt>n.perm</dt>
<dd>Numeric value specifying the number of permutations to perform.</dd>


<dt>verbose</dt>
<dd>Logical. If <code>TRUE</code>, progress messages are printed. 
Default is <code>FALSE</code>.</dd>

</dl>

estimateProb: Estimate the Empirical Probability of Whether Two Set of Cells from Distinct Batches Belong to the Same Population

Description

Usage

Value

Arguments

See Also