as.Seurat.CellDataSet

as.Seurat.SingleCellExperiment

Convert objects to <code>Seurat</code> objects

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

David Collins

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

Anagha Shenoy

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Brian Zhang

Shiwei Zheng

Satija Lab and Collaborators 

as.Seurat.CellDataSet function

<dl><dt>x</dt>
<dd>An object to convert to class <code>Seurat</code></dd>
<dt>slot</dt>
<dd>Slot to store expression data as</dd>
<dt>assay</dt>
<dd>Name of assays to convert; set to <code>NULL</code> for all assays to be converted</dd>
<dt>verbose</dt>
<dd>Show progress updates</dd>
<dt>...</dt>
<dd>Arguments passed to other methods</dd>
<dt>counts</dt>
<dd>name of the SingleCellExperiment assay to store as <code>counts</code>;
set to <code>NULL</code> if only normalized data are present</dd>
<dt>data</dt>
<dd>name of the SingleCellExperiment assay to slot as <code>data</code>.
Set to NULL if only counts are present</dd>
<dt>project</dt>
<dd>Project name for new Seurat object</dd></dl>

Arguments

Convert objects to Seurat objects — as.Seurat.CellDataSet

<dl>

<dt>x</dt>
<dd>An object to convert to class <code>Seurat</code></dd>


<dt>slot</dt>
<dd>Slot to store expression data as</dd>


<dt>assay</dt>
<dd>Name of assays to convert; set to <code>NULL</code> for all assays to be converted</dd>


<dt>verbose</dt>
<dd>Show progress updates</dd>


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


<dt>counts</dt>
<dd>name of the SingleCellExperiment assay to store as <code>counts</code>;
set to <code>NULL</code> if only normalized data are present</dd>


<dt>data</dt>
<dd>name of the SingleCellExperiment assay to slot as <code>data</code>.
Set to NULL if only counts are present</dd>


<dt>project</dt>
<dd>Project name for new Seurat object</dd>

</dl>

Convert objects to <code>Seurat</code> objects

as.Seurat.CellDataSet: Convert objects to `Seurat` objects

Description

Usage

Value

Arguments

See Also