identify_sex_metadata

Extract metadata for sex information if not provided already

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

identify_sex_metadata function

<dl><dt>container</dt>
<dd>environment Project container that stores sub-containers
for each cell type as well as results and plots from all analyses</dd>
<dt>y_gene</dt>
<dd>character Gene name to use for identifying male donors (default='RPS4Y1')</dd>
<dt>x_gene</dt>
<dd>character Gene name to use for identifying female donors (default='XIST')</dd></dl>

Arguments

Extract metadata for sex information if not provided already — identify_sex_metadata

<dl>

<dt>container</dt>
<dd>environment Project container that stores sub-containers
for each cell type as well as results and plots from all analyses</dd>


<dt>y_gene</dt>
<dd>character Gene name to use for identifying male donors (default='RPS4Y1')</dd>


<dt>x_gene</dt>
<dd>character Gene name to use for identifying female donors (default='XIST')</dd>

</dl>

identify_sex_metadata: Extract metadata for sex information if not provided already

Description

Usage

Value

Arguments