Introduction to MarkerGenes

Regina H. Reynolds

UCL

3 February 2023

Quick start to using to MarkerGenes

Brief description

Resource that contains data related to:

Resource also contains a number of functions that:

Please note that the above functions are only compatible with old-style EWCE specificity matrices.

What is gene specificity?

  • Specificity of a gene represents the proportion of the total expression of a gene found in one cell type as compared to that in all cell types (i.e., the mean expression in one cell type divided by the mean expression in all cell types). If the expression of a gene is shared between two or more cell types, it will get a lower specificity measure.
  • For a description of how it’s calculated, please refer to Skene et al. 2016.

Data structure

Structure of a specificity matrix

  • Each .rda file represents one single-cell dataset and typically contains two lists (some datasets may only have level 1 cell types). These two lists represent:
    • Level 1 cell types – broad cell type categories e.g. astrocyte, glutamatergic neuron, etc.
    • Level 2 cell types – subtypes of the broader cell type categories
  • With each of the two lists there are three additional lists, which typically have the same name.
    • annot: a character vector that provides the level 1 or level 2 cell type assigned to each single cell, which was used in the calculation
    • mean_exp: a matrix of mean expression for all genes (rows) across each cell type (columns)
    • specificity: a matrix of the specificity values for all genes (rows) across each cell type (columns)

Structure of a specificity dataframe

  • Dataframe of gene, tissue/cell-type, mean_expression, and specificity.

Citation

If you use any specificity matrices from this repository, please make sure you cite the original publication the specificity values were derived from. For details, please refer to: dataset metadata.

MarkerGenes can be cited using:

utils::citation("MarkerGenes")
#> 
#> To cite package 'MarkerGenes' in publications use:
#> 
#>   Reynolds RH (2023). _MarkerGenes_. doi:10.5281/zenodo.6418605
#>   <https://doi.org/10.5281/zenodo.6418605>,
#>   https://github.com/RHReynolds/MarkerGenes - R package version 0.99.1,
#>   <https://github.com/RHReynolds/MarkerGenes>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {MarkerGenes},
#>     author = {Regina H. Reynolds},
#>     year = {2023},
#>     url = {https://github.com/RHReynolds/MarkerGenes},
#>     note = {https://github.com/RHReynolds/MarkerGenes - R package version 0.99.1},
#>     doi = {10.5281/zenodo.6418605},
#>   }

Session info

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#>  tz       Europe/London
#>  date     2023-02-03
#>  pandoc   2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
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#> 
#> ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────