filterVector

Create logical filtering vector based on a numeric vector and a (sample-wise) cutoff

internal

Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'DoubletDetection' by Gayoso et al. (2020) <doi:10.5281/zenodo.2678041>. In the end, cells are filtered based on user input for use in downstream applications.

Rasmus Rydbirk

CRMetrics

Cell Ranger Output Filtering and Metrics Visualization

Fabienne Kick

Henrietta Holze

Xian Xin

filterVector function

<dl><dt>num.vec</dt>
<dd>numeric Numeric vector to create filter on</dd>
<dt>name</dt>
<dd>character Name of filter</dd>
<dt>filter</dt>
<dd>numeric Either a single numeric value or a numeric value with length of samples</dd>
<dt>samples</dt>
<dd>character Sample IDs</dd>
<dt>sep</dt>
<dd>character Separator to split cells by into sample-wise lists (default = "!!")</dd></dl>

Arguments

Create filtering vector — filterVector

<dl>

<dt>num.vec</dt>
<dd>numeric Numeric vector to create filter on</dd>


<dt>name</dt>
<dd>character Name of filter</dd>


<dt>filter</dt>
<dd>numeric Either a single numeric value or a numeric value with length of samples</dd>


<dt>samples</dt>
<dd>character Sample IDs</dd>


<dt>sep</dt>
<dd>character Separator to split cells by into sample-wise lists (default = "!!")</dd>

</dl>

filterVector: Create filtering vector

Description

Usage

Arguments