get_intersecting_pathways

Extract the intersection of gene sets which are enriched in two or more cell types for a factor

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_intersecting_pathways 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>factor_select</dt>
<dd>numeric The factor to investigate</dd>
<dt>these_ctypes_only</dt>
<dd>character A vector of cell types for which to get gene sets that are
enriched in all of these and not in any other cell types</dd>
<dt>up_down</dt>
<dd>character Set to "up" to get the gene sets for the positive loading genes. Set
to "down" to get the gene sets for the negative loadings genes.</dd>
<dt>thresh</dt>
<dd>numeric Pvalue significance threshold for selecting enriched sets (default=0.05)</dd></dl>

Arguments

Extract the intersection of gene sets which are enriched in two or more cell types for a factor — get_intersecting_pathways

<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>factor_select</dt>
<dd>numeric The factor to investigate</dd>


<dt>these_ctypes_only</dt>
<dd>character A vector of cell types for which to get gene sets that are
enriched in all of these and not in any other cell types</dd>


<dt>up_down</dt>
<dd>character Set to "up" to get the gene sets for the positive loading genes. Set
to "down" to get the gene sets for the negative loadings genes.</dd>


<dt>thresh</dt>
<dd>numeric Pvalue significance threshold for selecting enriched sets (default=0.05)</dd>

</dl>

get_intersecting_pathways: Extract the intersection of gene sets which are enriched in two or more cell types for a factor

Description

Usage

Value

Arguments