run_fgsea

Run fgsea for one cell type of one 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

run_fgsea 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 of interest</dd>
<dt>ctype</dt>
<dd>character The cell type of interest</dd>
<dt>db_use</dt>
<dd>character The database of gene sets to use. Database
options include "GO", "Reactome", "KEGG", "BioCarta", and "Hallmark". More than
one database can be used. (default="GO")</dd>
<dt>signed</dt>
<dd>logical If TRUE, uses signed gsea. If FALSE, uses unsigned gsea.
Currently only works with fgsea method. (default=TRUE)</dd>
<dt>min_gs_size</dt>
<dd>numeric Minimum gene set size (default=15)</dd>
<dt>max_gs_size</dt>
<dd>numeric Maximum gene set size (default=500)</dd>
<dt>ncores</dt>
<dd>numeric The number of cores to use (default=container$experiment_params$ncores)</dd></dl>

Arguments

Run fgsea for one cell type of one factor — run_fgsea

<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 of interest</dd>


<dt>ctype</dt>
<dd>character The cell type of interest</dd>


<dt>db_use</dt>
<dd>character The database of gene sets to use. Database
options include "GO", "Reactome", "KEGG", "BioCarta", and "Hallmark". More than
one database can be used. (default="GO")</dd>


<dt>signed</dt>
<dd>logical If TRUE, uses signed gsea. If FALSE, uses unsigned gsea.
Currently only works with fgsea method. (default=TRUE)</dd>


<dt>min_gs_size</dt>
<dd>numeric Minimum gene set size (default=15)</dd>


<dt>max_gs_size</dt>
<dd>numeric Maximum gene set size (default=500)</dd>


<dt>ncores</dt>
<dd>numeric The number of cores to use (default=container$experiment_params$ncores)</dd>

</dl>

run_fgsea: Run fgsea for one cell type of one factor

Description

Usage

Value

Arguments