Perform enrichR-style analysis on a screen

Usage

compute_multi_enrichr(
  data,
  genesets = NULL,
  species = NULL,
  direction = "both",
  p_value_cutoff = 0.01,
  n_distinct = 10
)

Arguments

data: A tidyseurat object merged with metadata. Must contain columns "Well_ID", "Row", "Column".
genesets: Named list of genes
species: One of "human", "mouse", "fly", "yeast", "worm" or "fish"
direction: Direction of the differentially expressed genes, one of "up", "down", "both" (default).
p_value_cutoff: Cutoff for adjusted p-value (column p_value_adj), default 0.01
n_distinct: Minimum number of genes in a geneset, default 5

Value

A tidyseurat object with appended pathway_enrichment dataframe in slot tools

Examples

data(mini_mac)
data(genesets)
compute_multi_enrichr(mini_mac, genesets = genesets)
#> # A Seurat-tibble abstraction: 308 × 21
#> # Features=500 | Cells=308 | Active assay=RNA | Assays=RNA
#>    .cell      orig.ident   nCount_RNA nFeature_RNA Plate_ID Well_ID Row   Column
#>    <chr>      <fct>             <dbl>        <int> <chr>    <chr>   <chr>  <int>
#>  1 AACAGGCAAT PMMSq033_mi…         65           29 PMMSq033 B02     B          2
#>  2 AACCAGCCAG PMMSq033_mi…        522           97 PMMSq033 C02     C          2
#>  3 AACCAGTTGA PMMSq033_mi…        415           82 PMMSq033 D02     D          2
#>  4 AACCGGCGTA PMMSq033_mi…        578           93 PMMSq033 E02     E          2
#>  5 AACCTAGTCC PMMSq033_mi…        286           72 PMMSq033 F02     F          2
#>  6 AACTCTACAC PMMSq033_mi…        515           96 PMMSq033 G02     G          2
#>  7 AACTGTGTCA PMMSq033_mi…        408           87 PMMSq033 H02     H          2
#>  8 AAGATGTCCA PMMSq033_mi…        332           78 PMMSq033 I02     I          2
#>  9 AAGCATATGG PMMSq033_mi…        498           92 PMMSq033 J02     J          2
#> 10 AAGCTCACCT PMMSq033_mi…        539          102 PMMSq033 K02     K          2
#> # ℹ 298 more rows
#> # ℹ 13 more variables: Species <chr>, Cell_type <chr>, Model_type <chr>,
#> #   Time <fct>, Unit <chr>, Treatment_1 <chr>, Concentration_1 <fct>,
#> #   Unit_1 <chr>, Sample_type <chr>, Project <chr>, combined_id <chr>,
#> #   percent.mt <dbl>, percent.ribo <dbl>