getSignatureEnrichment | R Documentation |
Extracts the names of enriched gene sets by cluster signature.
getSignatureEnrichment(
object,
across = getDefaultGrouping(object, verbose = TRUE, "across"),
across_subset = NULL,
n_gsets = 10,
signif_var = "fdr",
signif_threshold = 0.05,
method_de = NULL
)
object |
An object of class |
across |
Character value or NULL. Specifies the grouping variable of interest. Use |
across_subset |
Character vector or NULL. Specifies the particular groups
of interest the grouping variable specified in argument 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 |
n_gsets |
Numeric value. Maximal number of gene sets whose results are included.
The first |
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 |
method_de |
Character value. Denotes the method to according to which the de-analysis is performed.
Given to argument |
A named list of character vectors.
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