getfdata

This functions allows the extraction of a filtered and normalized expression matrix

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <DOI:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <DOI:10.1186/s13059-023-02974-1>).

Dominic Grc3<bc>n

RaceID

Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Dominic Grün

getfdata function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>g</dt>
<dd>Vector of gene names to be included corresponding to a subset of valid row names of the <code>ndata</code> slot
of the <code>SCseq</code> object. Default is <code>NULL</code> and data for all genes remaining after filtering by the <code>filterdata</code> function are shown.</dd>
<dt>n</dt>
<dd>Vector of valid column names corresponding to a subset of valid column names of the <code>ndata</code> slot
of the <code>SCseq</code> object. Default is <code>NULL</code> and data for all cells remaining after filtering by the <code>filterdata</code> function are shown.</dd></dl>

Arguments

Extracting filtered expression data — getfdata

<dl>

<dt>object</dt>
<dd><code>SCseq</code> class object.</dd>


<dt>g</dt>
<dd>Vector of gene names to be included corresponding to a subset of valid row names of the <code>ndata</code> slot
of the <code>SCseq</code> object. Default is <code>NULL</code> and data for all genes remaining after filtering by the <code>filterdata</code> function are shown.</dd>


<dt>n</dt>
<dd>Vector of valid column names corresponding to a subset of valid column names of the <code>ndata</code> slot
of the <code>SCseq</code> object. Default is <code>NULL</code> and data for all cells remaining after filtering by the <code>filterdata</code> function are shown.</dd>

</dl>

getfdata: Extracting filtered expression data

Description

Usage

Value

Arguments