normalize_counts

Helper function to normalize and log-transform count 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

normalize_counts function

<dl><dt>count_data</dt>
<dd>matrix or sparse matrix Gene by cell matrix of counts</dd>
<dt>scale_factor</dt>
<dd>numeric The number that gets multiplied by fractional counts
during normalization of the pseudobulked data (default=10000)</dd></dl>

Arguments

Helper function to normalize and log-transform count data — normalize_counts

<dl>

<dt>count_data</dt>
<dd>matrix or sparse matrix Gene by cell matrix of counts</dd>


<dt>scale_factor</dt>
<dd>numeric The number that gets multiplied by fractional counts
during normalization of the pseudobulked data (default=10000)</dd>

</dl>

normalize_counts: Helper function to normalize and log-transform count data

Description

Usage

Value

Arguments