Obtain enrichment results

Extracts the results from gene set enrichment analysis in form of either a list (if reduce was set to TRUE) or an object of class hyp (if reduce was set to FALSE).

getGseaResults(
  object,
  across = getDefaultGrouping(object, verbose = TRUE, "across"),
  across_subset = NULL,
  method_de = NULL,
  flatten = TRUE,
  stop_if_null = TRUE,
  assay_name = activeAssay(object)
)

Arguments

object

An object of class SPATA2 or, in case of S4 generics, objects of classes for which a method has been defined.

across

Character value or NULL. Specifies the grouping variable of interest.

Use getGroupingOptions() to obtain all variable names that group the barcode spots of your object in a certain manner.

across_subset

Character vector or NULL. Specifies the particular groups of interest the grouping variable specified in argument across contains.

If set to NULL all of them are chosen. You can prefix groups you are NOT interested in with a '-'. (Saves writing if there are more groups you are interested in than groups you are not interested in.)

Use getGroupNames() to obtain all valid input options.

method_de

Character value. Denotes the method to according to which the de-analysis is performed. Given to argument test.use of the Seurat::FindAllMarkers()-function. Run SPATA::dea_methods to obtain all valid input options.

Value

A list or an object of class hyp.