project_new_data

Project multicellular patterns to get scores on new data

Single-cell Interpretable Tensor Decomposition (scITD) employs the
Tucker tensor decomposition to extract multicell-type gene expression patterns
that vary across donors/individuals. This tool is geared for use with single-cell
RNA-sequencing datasets consisting of many source donors. The method has a wide
range of potential applications, including the study of inter-individual variation
at the population-level, patient sub-grouping/stratification, and the analysis
of sample-level batch effects. Each "multicellular process" that is extracted
consists of (A) a multi cell type gene loadings matrix and (B) a
corresponding donor scores vector indicating the level at which the corresponding
loadings matrix is expressed in each donor. Additional methods are implemented
to aid in selecting an appropriate number of factors and to evaluate stability
of the decomposition. Additional tools are provided for downstream analysis,
including integration of gene set enrichment analysis and ligand-receptor analysis.
Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Jonathan Mitchel

scITD

Single-Cell Interpretable Tensor Decomposition

Evan Biederstedt

Peter Kharchenko

project_new_data function

<dl><dt>new_container</dt>
<dd>environment A project container with new data to project scores
for. The form_tensor() function should be run.</dd>
<dt>old_container</dt>
<dd>environment The original project container that has the multicellular
gene expression patterns already extracted. These patterns will be projected onto the new data.</dd></dl>

Arguments

Project multicellular patterns to get scores on new data — project_new_data

<dl>

<dt>new_container</dt>
<dd>environment A project container with new data to project scores
for. The form_tensor() function should be run.</dd>


<dt>old_container</dt>
<dd>environment The original project container that has the multicellular
gene expression patterns already extracted. These patterns will be projected onto the new data.</dd>

</dl>

project_new_data: Project multicellular patterns to get scores on new data

Description

Usage

Value

Arguments