ref_adj

Take in a data.table of genomic positions and smoothed, centered expression intensities counts and
adjust for reference beads by subtracting average intensities of reference beads for each gene.
This is the second reference adjustment.

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 

ref_adj function

<dl><dt>centered_rm</dt>
<dd>data.table of smoothed, centered expression intensities counts</dd>
<dt>normal_beads</dt>
<dd>vector of names of normal beads</dd></dl>

Arguments

Adjust for Reference (Normal) Beads — ref_adj

<dl>

<dt>centered_rm</dt>
<dd>data.table of smoothed, centered expression intensities counts</dd>


<dt>normal_beads</dt>
<dd>vector of names of normal beads</dd>

</dl>

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ref_adj: Adjust for Reference (Normal) Beads

Description

Usage

Value

Arguments