enrichment_in_groups — enrichment_in

Calculate the enrichment in pathways using Fisher's exact or Kolmogorov-Smirnov test, using either the abundance column to identify feature or the targets list. access through leapr wrapper

Usage

enrichment_in_groups(
  geneset,
  targets = c(),
  background = NULL,
  assay_name = NULL,
  method = "fishers",
  minsize = 5,
  mapping_column = NULL,
  abundance_column = NULL,
  randomize = FALSE,
  silence_try_errors = TRUE
)

Arguments

geneset: geneset to use for enrichment
targets: targets to use for enrichment
background: `SummarizedExperiment` describing background to use
assay_name: is the name of the assay to use from the background
method: method to use for statistical test, options are 'fishers', 'ks', 'ztest', or 'chisq'. Remember that KS test assumes normality, so it would be good to log your data before calling. NOTE: if you do not call `suppressWarnings` then the KS test will warn you about ties.
minsize: minimum size of set
mapping_column: column name of mapping identifiers
abundance_column: columns mapping abundance, either in the `assay` matrix or `rowData`
randomize: true/false whether to randomize
silence_try_errors: true/false to silence errors

Value

data frame with enrichment results