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Cell types based on overlap of marker genes

Source: R/overlaps.R
clustermole_overlaps.Rd

Perform overrepresentation analysis for a set of genes compared to all cell type signatures.

Usage

clustermole_overlaps(genes, species)

Arguments

genes

A character vector of gene symbols.

species

Gene symbol species: hs for human or mm for mouse.

Value

A data frame with one row per returned signature:

  • overlap: Unique gene count shared by the input and signature.

  • p_value: Hypergeometric test p-value.

  • fdr: Benjamini-Hochberg adjusted p-value across all tested signatures.

  • n_genes: Unique gene count in the signature for the requested species.

  • Signature metadata (see clustermole_markers()).

Examples

my_genes <- c("CD2", "CD3D", "CD3E", "CD3G", "TRAC", "TRBC2", "LTB")
my_overlaps <- clustermole_overlaps(genes = my_genes, species = "hs")
head(my_overlaps)
#> # A tibble: 6 × 9
#>   celltype_full   db    species organ celltype n_genes overlap  p_value      fdr
#>   <chr>           <chr> <chr>   <chr> <chr>      <int>   <dbl>    <dbl>    <dbl>
#> 1 CD4+ T cell (G… Cell… "HS"    Stom… CD4+ T …      23       7 4.13e-22 4.93e-18
#> 2 Effector CD4+ … ScTy… ""      Immu… Effecto…      27       7 1.50e-21 4.93e-18
#> 3 Naive CD4+ T c… ScTy… ""      Immu… Naive C…      27       7 1.50e-21 4.93e-18
#> 4 Memory CD4+ T … ScTy… ""      Immu… Memory …      28       7 1.99e-21 4.93e-18
#> 5 Effector CD8+ … ScTy… ""      Immu… Effecto…      29       7 2.63e-21 4.93e-18
#> 6 Naive CD8+ T c… ScTy… ""      Immu… Naive C…      29       7 2.63e-21 4.93e-18