getGseaDf: Obtain enrichment data.frame
In theMILOlab/SPATA2: A Toolbox for Spatial Expression Analysis

getGseaDf

R Documentation

Obtain enrichment data.frame

Description

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

Usage

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.