prep_cnv_dat

This function caps CNV scores, adds annotation columns for plotting,
performs hierarchical clustering of bins based on similar CNV score, and plots nUMI per bin

This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").

Diane Zhang

SlideCNA

Calls Copy Number Alterations from Slide-Seq Data

Johanna Klughammer

Jan Watter

Broad Institute of MIT and Harvard 

prep_cnv_dat function

<dl><dt>dat_bin</dt>
<dd>data.table of CNV scores per bin</dd>
<dt>lower</dt>
<dd>numeric float to represent the lower cap for CNV scores</dd>
<dt>upper</dt>
<dd>numeric float to represent the upper cap for CNV scores</dd>
<dt>hc_function</dt>
<dd>character for which hierarchical clustering function to use</dd>
<dt>plot_directory</dt>
<dd>output plot directory path</dd></dl>

Arguments

Prepare data for CNV heat map — prep_cnv_dat

<dl>

<dt>dat_bin</dt>
<dd>data.table of CNV scores per bin</dd>


<dt>lower</dt>
<dd>numeric float to represent the lower cap for CNV scores</dd>


<dt>upper</dt>
<dd>numeric float to represent the upper cap for CNV scores</dd>


<dt>hc_function</dt>
<dd>character for which hierarchical clustering function to use</dd>


<dt>plot_directory</dt>
<dd>output plot directory path</dd>

</dl>

prep_cnv_dat: Prepare data for CNV heat map

Description

Usage

Value

Arguments