get_max_correlations

Computes the max correlation between each factor of the decomposition done using
the whole dataset to each factor computed using the subsampled/bootstrapped dataset

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

get_max_correlations function

<dl><dt>res_full</dt>
<dd>matrix Either the donor scores or loadings matrix from the original
decomposition</dd>
<dt>res_sub</dt>
<dd>matrix Either the donor scores or loadings matrix from the new
decomposition</dd>
<dt>res_use</dt>
<dd>character Can either be 'loadings' or 'dscores' and should correspond
with the data matrix used</dd></dl>

Arguments

Computes the max correlation between each factor of the decomposition done using
the whole dataset to each factor computed using the subsampled/bootstrapped dataset — get_max_correlations

<dl>

<dt>res_full</dt>
<dd>matrix Either the donor scores or loadings matrix from the original
decomposition</dd>


<dt>res_sub</dt>
<dd>matrix Either the donor scores or loadings matrix from the new
decomposition</dd>


<dt>res_use</dt>
<dd>character Can either be 'loadings' or 'dscores' and should correspond
with the data matrix used</dd>

</dl>

Computes the max correlation between each factor of the decomposition done using
the whole dataset to each factor computed using the subsampled/bootstrapped dataset

get_max_correlations: Computes the max correlation between each factor of the decomposition done using the whole dataset to each factor computed using the subsampled/bootstrapped dataset

Description

Usage

Value

Arguments