scale_nUMI

This function re-scales expression intensities to be in a smaller range, normalizes for nUMI per bin,
and subtracts reference bead signal

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 

scale_nUMI function

<dl><dt>dat_bin</dt>
<dd>data.table of relative expression intensities per bin</dd>
<dt>thresh_hard</dt>
<dd>TRUE if using strict thresholds for expression thresholds and FALSE if adjusting
thresholds based on 1 + or - the mean of absolute min and max values</dd></dl>

Arguments

Scale for nUMI (UMI Count) to generate CNV scores — scale_nUMI

<dl>

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


<dt>thresh_hard</dt>
<dd>TRUE if using strict thresholds for expression thresholds and FALSE if adjusting
thresholds based on 1 + or - the mean of absolute min and max values</dd>

</dl>

scale_nUMI: Scale for nUMI (UMI Count) to generate CNV scores

Description

Usage

Value

Arguments