prep

This function takes in a data table of raw counts and a vector of reference/normal beads
to normalize counts and adjust for reference expression.

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 function

<dl><dt>so</dt>
<dd>Seurat object of Slide-seq data with raw counts</dd>
<dt>normal_beads</dt>
<dd>vector of names of normal beads</dd>
<dt>gene_pos</dt>
<dd>data.table with columns for GENE, chr, start, end, rel_gene_pos (1 : # of genes on chromosome)</dd>
<dt>chrom_ord</dt>
<dd>vector of the names of chromosomes in order</dd>
<dt>logTPM</dt>
<dd>TRUE if performing adjustment with logTPM</dd></dl>

Arguments

Infercnv-based preparation of relative gene expression intensities — prep

<dl>

<dt>so</dt>
<dd>Seurat object of Slide-seq data with raw counts</dd>


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


<dt>gene_pos</dt>
<dd>data.table with columns for GENE, chr, start, end, rel_gene_pos (1 : # of genes on chromosome)</dd>


<dt>chrom_ord</dt>
<dd>vector of the names of chromosomes in order</dd>


<dt>logTPM</dt>
<dd>TRUE if performing adjustment with logTPM</dd>

</dl>

prep: Infercnv-based preparation of relative gene expression intensities

Description

Usage

Value

Arguments