scaleNotCenter

This function scales normalized gene expression data after variable genes have been selected.
Note that the data is not mean-centered before scaling because expression values must remain
positive (NMF only accepts positive values). It also removes cells which do not have any
expression across the genes selected, by default.

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Yichen Wang

rliger

Linked Inference of Genomic Experimental Relationships

Joshua Welch

Chao Gao

Jialin Liu

Joshua Sodicoff

Velina Kozareva

Evan Macosko

Paul Hoffman

Ilya Korsunsky

Robert Lee

scaleNotCenter function

<dl><dt>object</dt>
<dd><code>liger</code> object. Should call normalize and selectGenes before calling.</dd>
<dt>remove.missing</dt>
<dd>Whether to remove cells from scale.data with no gene expression
(default TRUE).</dd>
<dt>chunk</dt>
<dd>size of chunks in hdf5 file. (default 1000)</dd>
<dt>verbose</dt>
<dd>Print progress bar/messages (TRUE by default)</dd></dl>

Arguments

Scale genes by root-mean-square across cells — scaleNotCenter

<dl>

<dt>object</dt>
<dd><code>liger</code> object. Should call normalize and selectGenes before calling.</dd>


<dt>remove.missing</dt>
<dd>Whether to remove cells from scale.data with no gene expression
(default TRUE).</dd>


<dt>chunk</dt>
<dd>size of chunks in hdf5 file. (default 1000)</dd>


<dt>verbose</dt>
<dd>Print progress bar/messages (TRUE by default)</dd>

</dl>

Scale genes by root-mean-square across cells

scaleNotCenter: Scale genes by root-mean-square across cells

Description

Usage

Value

Arguments

Examples