weight_rollmean

Take in a data.table of genomic positions and bead normalized/modified counts and apply pyramidal weighting
with a window size k to create smoothed expression intensities

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 

weight_rollmean function

<dl><dt>dat</dt>
<dd>data.table of normalized/adjusted counts</dd>
<dt>k</dt>
<dd>size of window for weighting</dd></dl>

Arguments

Expressional smoothing along a chromosome using a weighted pyramidal moving average — weight_rollmean

<dl>

<dt>dat</dt>
<dd>data.table of normalized/adjusted counts</dd>


<dt>k</dt>
<dd>size of window for weighting</dd>

</dl>

weight_rollmean: Expressional smoothing along a chromosome using a weighted pyramidal moving average

Description

Usage

Value

Arguments