createSRT

An independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in 'SRTsim': reference-based and reference-free.

Jiaqiang Zhu

SRTsim

Simulator for Spatially Resolved Transcriptomics

Lulu Shang

Xiang Zhou

createSRT function

<dl><dt>count_in</dt>
<dd>A gene expression count <code>matrix</code></dd>
<dt>loc_in</dt>
<dd>A location <code>dataframe</code> with colnames x,y,label</dd>
<dt>refID</dt>
<dd>A <code>character</code> reference sample identifier. Default = <code>ref1</code>.</dd></dl>

Arguments

Create simSRT object — createSRT

<dl>

<dt>count_in</dt>
<dd>A gene expression count <code>matrix</code></dd>


<dt>loc_in</dt>
<dd>A location <code>dataframe</code> with colnames x,y,label</dd>


<dt>refID</dt>
<dd>A <code>character</code> reference sample identifier. Default = <code>ref1</code>.</dd>

</dl>

createSRT: Create simSRT object

Description

Usage

Value

Arguments

Examples