downsampling

Downsampling cells from each group for IDER-based similarity
calculation.

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

downsampling function

<dl><dt>metadata</dt>
<dd>Data frame. It includes at least 2 columns, label and batch.
Each row corresponds to one cell. Required.</dd>
<dt>n.size</dt>
<dd>Numeric. The number of cells used in each group. (Default: 35)</dd>
<dt>seed</dt>
<dd>Numeric. Seed used to sample. (Default: 12345)</dd>
<dt>include</dt>
<dd>Boolean. Using `include = TRUE` to include the group smaller
than required size. (Default: FALSE)</dd>
<dt>replace</dt>
<dd>Boolean. Using `replace = TRUE` if the group is smaller than
required size and some cells will be repeatedly used. (Default: FALSE)</dd>
<dt>lower.cutoff</dt>
<dd>Numeric. The minimum size of groups to keep.
(Default: 3)</dd></dl>

Arguments

Downsampling cells — downsampling

<dl>

<dt>metadata</dt>
<dd>Data frame. It includes at least 2 columns, label and batch.
Each row corresponds to one cell. Required.</dd>


<dt>n.size</dt>
<dd>Numeric. The number of cells used in each group. (Default: 35)</dd>


<dt>seed</dt>
<dd>Numeric. Seed used to sample. (Default: 12345)</dd>


<dt>include</dt>
<dd>Boolean. Using `include = TRUE` to include the group smaller
than required size. (Default: FALSE)</dd>


<dt>replace</dt>
<dd>Boolean. Using `replace = TRUE` if the group is smaller than
required size and some cells will be repeatedly used. (Default: FALSE)</dd>


<dt>lower.cutoff</dt>
<dd>Numeric. The minimum size of groups to keep.
(Default: 3)</dd>

</dl>

downsampling: Downsampling cells

Description

Usage

Value

Arguments