getFilteredCounts

This function discards lowly expressed genes from a count matrix stored in an <code>SCseq</code> object.

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

getFilteredCounts function

<dl><dt>object</dt>
<dd><code>SCseq</code> class object.</dd>
<dt>minnumber</dt>
<dd>Integer number greater or equal to zero. Minimum number of cells required to have at least <code>minexpr</code> transcript counts for a gene to not be discarded. Default is 5.</dd>
<dt>minexpr</dt>
<dd>Integer number greater or equal to zero. Minimum expression of a gene in at least <code>minnumber</code> cells to not be discarded. Default is 5.</dd></dl>

Arguments

Function for filtering count data — getFilteredCounts

<dl>

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


<dt>minnumber</dt>
<dd>Integer number greater or equal to zero. Minimum number of cells required to have at least <code>minexpr</code> transcript counts for a gene to not be discarded. Default is 5.</dd>


<dt>minexpr</dt>
<dd>Integer number greater or equal to zero. Minimum expression of a gene in at least <code>minnumber</code> cells to not be discarded. Default is 5.</dd>

</dl>

getFilteredCounts: Function for filtering count data

Description

Usage

Value

Arguments