reduceNoise

Simple filter for removing noise in single-cell data.

Deconvolution of bulk RNA-Sequencing data into proportions of cells based on a reference single-cell RNA-Sequencing dataset using high-dimensional geometric methodology.

Myles Lewis

cellGeometry

Geometric Single Cell Deconvolution

Rachel Lau

reduceNoise function

<dl><dt>cellmat</dt>
<dd>Matrix of log2 mean gene expression in rows with cell types in
columns.</dd>
<dt>noisefilter</dt>
<dd>Sets an upper bound for <code>noisefraction</code> cut-off below
which gene expression is set to 0. Essentially gene expression above this
level must be retained in the signature. Setting this higher can allow more
suppression via <code>noisefraction</code> and can favour more highly expressed genes.</dd>
<dt>noisefraction</dt>
<dd>Numeric value. Maximum mean log2 gene expression across
cell types is calculated and values in celltypes below this fraction are
set to 0. Set in conjunction with <code>noisefilter.</code> Note: if this is set too
high (too close to 1), it can have a deleterious effect on deconvolution.</dd></dl>

Arguments

Reduce noise in single-cell data — reduceNoise

<dl>

<dt>cellmat</dt>
<dd>Matrix of log2 mean gene expression in rows with cell types in
columns.</dd>


<dt>noisefilter</dt>
<dd>Sets an upper bound for <code>noisefraction</code> cut-off below
which gene expression is set to 0. Essentially gene expression above this
level must be retained in the signature. Setting this higher can allow more
suppression via <code>noisefraction</code> and can favour more highly expressed genes.</dd>


<dt>noisefraction</dt>
<dd>Numeric value. Maximum mean log2 gene expression across
cell types is calculated and values in celltypes below this fraction are
set to 0. Set in conjunction with <code>noisefilter.</code> Note: if this is set too
high (too close to 1), it can have a deleterious effect on deconvolution.</dd>

</dl>

reduceNoise: Reduce noise in single-cell data

Description

Usage

Value

Arguments