Obtain enrichment data.frame

Extracts results from a gene set enrichment analysis in form of a data.frame.

getGseaDf(
  object,
  across,
  across_subset = NULL,
  method_de = NULL,
  n_gsets = Inf,
  signif_var = "fdr",
  signif_threshold = 1,
  stop_if_null = TRUE
)

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.

n_gsets

Numeric value. Maximal number of gene sets whose results are included. The first n_gsets are included starting with the one with the lowest significance value.

signif_var

Character value. Determines what to be considered while checking for significance. Either 'pval' (p-Value) or 'fdr' (False Discovery Rate).

signif_threshold

Numeric value. Significance values below signif_threshold are not included.

Value

Data.frame that contains results of gene set enrichment analysis.