make_so_bin

Aggregate Seurat object counts by bin to create a new Seurat object with binned beads
as units instead of beads

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 

make_so_bin function

<dl><dt>so</dt>
<dd>Seurat object of beads and their meta data</dd>
<dt>md</dt>
<dd>data.frame of metadata for Seurat object</dd>
<dt>hcl_sub</dt>
<dd>hierarchical clustering object of cluster assignemnt as outputted from SlideCNA::plot_clones()</dd>
<dt>mal</dt>
<dd>TRUE if using malignant beads only</dd></dl>

Arguments

Make a binned version of a Seurat object — make_so_bin

<dl>

<dt>so</dt>
<dd>Seurat object of beads and their meta data</dd>


<dt>md</dt>
<dd>data.frame of metadata for Seurat object</dd>


<dt>hcl_sub</dt>
<dd>hierarchical clustering object of cluster assignemnt as outputted from SlideCNA::plot_clones()</dd>


<dt>mal</dt>
<dd>TRUE if using malignant beads only</dd>

</dl>

make_so_bin: Make a binned version of a Seurat object

Description

Usage

Value

Arguments