runPCAQueryAlone

Runs a standard PCA pipeline on query (1 batch). Assumes query_exp is already normalized.

Implements the Symphony single-cell reference building and query mapping algorithms and additional functions described in Kang et al <https://www.nature.com/articles/s41467-021-25957-x>.

Joyce Kang

symphony

Efficient and Precise Single-Cell Reference Atlas Mapping

Ilya Korsunsky

Soumya Raychaudhuri

runPCAQueryAlone function

<dl><dt>query_exp</dt>
<dd>Query expression matrix (genes x cells)</dd>
<dt>topn</dt>
<dd>Number of variable genes to use</dd>
<dt>d</dt>
<dd>Number of dimensions</dd>
<dt>seed</dt>
<dd>random seed</dd></dl>

Arguments

Runs a standard PCA pipeline on query (1 batch). Assumes query_exp is already normalized. — runPCAQueryAlone

<dl>

<dt>query_exp</dt>
<dd>Query expression matrix (genes x cells)</dd>


<dt>topn</dt>
<dd>Number of variable genes to use</dd>


<dt>d</dt>
<dd>Number of dimensions</dd>


<dt>seed</dt>
<dd>random seed</dd>

</dl>

runPCAQueryAlone: Runs a standard PCA pipeline on query (1 batch). Assumes query_exp is already normalized.

Description

Usage

Value

Arguments