center_rm

Take in a data.table of genomic positions and smoothed expression intensities counts and center by
subtracting average intensity across all beads for each gene

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 

center_rm function

<dl><dt>rm</dt>
<dd>data.table of smoothed expression intensities counts</dd></dl>

Arguments

Center expression intensities — center_rm

<dl>

<dt>rm</dt>
<dd>data.table of smoothed expression intensities counts</dd>

</dl>

center_rm: Center expression intensities

Description

Usage

Value

Arguments