SketchData

This function uses sketching methods to downsample high-dimensional single-cell RNA expression data,
which can help with scalability for large datasets.

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Andrew Butler

Saket Choudhary

Charlotte Darby

Jeff Farrell

Isabella Grabski

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Longda Jiang

Madeline Kowalski

Skylar Li

Gesmira Molla

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

SketchData function

<dl><dt>object</dt>
<dd>A Seurat object.</dd>
<dt>assay</dt>
<dd>Assay name. Default is NULL, in which case the default assay of the object is used.</dd>
<dt>ncells</dt>
<dd>A positive integer indicating the number of cells to sample for the sketching. Default is 5000.</dd>
<dt>sketched.assay</dt>
<dd>Sketched assay name. A sketch assay is created or overwrite with the sketch data. Default is 'sketch'.</dd>
<dt>method</dt>
<dd>Sketching method to use. Can be 'LeverageScore' or 'Uniform'.
Default is 'LeverageScore'.</dd>
<dt>var.name</dt>
<dd>A metadata column name to store the leverage scores. Default is 'leverage.score'.</dd>
<dt>over.write</dt>
<dd>whether to overwrite existing column in the metadata. Default is FALSE.</dd>
<dt>seed</dt>
<dd>A positive integer for the seed of the random number generator. Default is 123.</dd>
<dt>cast</dt>
<dd>The type to cast the resulting assay to. Default is 'dgCMatrix'.</dd>
<dt>verbose</dt>
<dd>Print progress and diagnostic messages</dd>
<dt>...</dt>
<dd>Arguments passed to other methods</dd></dl>

Arguments

Sketch Data — SketchData

<dl>

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


<dt>assay</dt>
<dd>Assay name. Default is NULL, in which case the default assay of the object is used.</dd>


<dt>ncells</dt>
<dd>A positive integer indicating the number of cells to sample for the sketching. Default is 5000.</dd>


<dt>sketched.assay</dt>
<dd>Sketched assay name. A sketch assay is created or overwrite with the sketch data. Default is 'sketch'.</dd>


<dt>method</dt>
<dd>Sketching method to use. Can be 'LeverageScore' or 'Uniform'.
Default is 'LeverageScore'.</dd>


<dt>var.name</dt>
<dd>A metadata column name to store the leverage scores. Default is 'leverage.score'.</dd>


<dt>over.write</dt>
<dd>whether to overwrite existing column in the metadata. Default is FALSE.</dd>


<dt>seed</dt>
<dd>A positive integer for the seed of the random number generator. Default is 123.</dd>


<dt>cast</dt>
<dd>The type to cast the resulting assay to. Default is 'dgCMatrix'.</dd>


<dt>verbose</dt>
<dd>Print progress and diagnostic messages</dd>


<dt>...</dt>
<dd>Arguments passed to other methods</dd>

</dl>

Sketch Data

SketchData: Sketch Data

Description

Usage

Value

Arguments