cellmarker_enrich

This function uses the CellMarker and Panglao datasets to identify cell-type differentially expressed genes.

The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. <doi:10.1093/nargab/lqab011>.

Dustin Sokolowski

scMappR

Single Cell Mapper

Mariela Faykoo-Martinez

Lauren Erdman

Houyun Hou

Cadia Chan

Helen Zhu

Melissa Holmes

Anna Goldenberg

Michael Wilson

cellmarker_enrich function

<dl><dt>gene_list</dt>
<dd>A character vector of gene symbols with the same designation (e.g. mouse symbol - mouse, human symbol - human) as the gene set database.</dd>
<dt>p_thresh</dt>
<dd>The Fisher's test cutoff for a cell-marker to be enriched.</dd>
<dt>gmt</dt>
<dd>Either a path to an rda file containing an object called "gmt", which is a named list where each element of the list is a vector of gene symbols website for more detail on the file type (https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats). The gmt list may also be inputted.</dd>
<dt>fixed_length</dt>
<dd>Estimated number of genes in your background.</dd>
<dt>min_genes</dt>
<dd>Minimum number of genes in the cell-type markers.</dd>
<dt>max_genes</dt>
<dd>Maximum number of genes in the cell-type markers.</dd>
<dt>isect_size</dt>
<dd>Number of genes in your list and the cell-type.</dd></dl>

Arguments

Fisher's Exact Cell-Type Identification. — cellmarker_enrich

<dl>

<dt>gene_list</dt>
<dd>A character vector of gene symbols with the same designation (e.g. mouse symbol - mouse, human symbol - human) as the gene set database.</dd>


<dt>p_thresh</dt>
<dd>The Fisher's test cutoff for a cell-marker to be enriched.</dd>


<dt>gmt</dt>
<dd>Either a path to an rda file containing an object called "gmt", which is a named list where each element of the list is a vector of gene symbols website for more detail on the file type (https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats). The gmt list may also be inputted.</dd>


<dt>fixed_length</dt>
<dd>Estimated number of genes in your background.</dd>


<dt>min_genes</dt>
<dd>Minimum number of genes in the cell-type markers.</dd>


<dt>max_genes</dt>
<dd>Maximum number of genes in the cell-type markers.</dd>


<dt>isect_size</dt>
<dd>Number of genes in your list and the cell-type.</dd>

</dl>

Fisher's Exact Cell-Type Identification.

cellmarker_enrich: Fisher's Exact Cell-Type Identification.

Description

Usage

Value

Arguments

Details

Examples