Calculate Gini marker specificity

Calculate Gini marker specificity.

findGiniMarkers(
  object,
  features = NULL,
  group.by = "seurat_clusters",
  assay = NULL,
  min.pct = 0.1,
  verbose = T
)

Arguments

object

Seurat object

features

feature to run gini specificy scoring on.

group.by

groups used for feature specificity assignment. E.g., Each gene is assigned to a single group in which it exhibits maximal specificity. Default is 'seurat_clusters'.

assay

Assay to run gini specificity scoring on. Default is DefaultAssay(object).

min.pct

minimal expression fraction per group. Gini scoring performs poorly on genes expressed at extremely low levels. Default (recommended) is 0.1.

verbose

print progress. Default is T.

Value

data.frame with feature-specific gini scores.

See also

fdrtool for p values calculations, ineq for gini index calculations.

Author

Nicholas Mikolajewicz