findGiniMarkers: Calculate Gini marker specificity

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Calculate Gini marker specificity

Description

Calculate Gini marker specificity.

Usage

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.

Author(s)

Nicholas Mikolajewicz

See Also

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

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.