scalefit

This function re-scales expression intensities to be in a smaller range, normalizes for nUMI per bin,
and centers the CNV scores to have a mean of 1

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 

scalefit function

<dl><dt>obj</dt>
<dd>data.table of relative expression intensities per bin</dd>
<dt>nbin</dt>
<dd>nUMIs in that specific bin</dd>
<dt>start</dt>
<dd>lower bound of CNV scores</dd>
<dt>end</dt>
<dd>upper bound of CNV scores</dd></dl>

Arguments

Subfunction for scale_nUMI that normalizes a given bin for UMI count and centers the  mean CNV score at 1 — scalefit

<dl>

<dt>obj</dt>
<dd>data.table of relative expression intensities per bin</dd>


<dt>nbin</dt>
<dd>nUMIs in that specific bin</dd>


<dt>start</dt>
<dd>lower bound of CNV scores</dd>


<dt>end</dt>
<dd>upper bound of CNV scores</dd>

</dl>

scalefit: Subfunction for scale_nUMI that normalizes a given bin for UMI count and centers the mean CNV score at 1

Description

Usage

Value

Arguments