scCustomize (version 3.1.3)

MAD_Stats: Median Absolute Deviation Statistics

Description

Get quick values for X x median absolute deviation for Genes, UMIs, %mito per cell grouped by meta.data variable.

Usage

MAD_Stats(
  seurat_object,
  group_by_var = deprecated(),
  group.by = "orig.ident",
  default_var = TRUE,
  mad_var = NULL,
  mad_num = 2
)

Value

A data.frame.

Arguments

seurat_object

Seurat object name.

group_by_var

soft-deprecated. See group.by.

group.by

meta data column to classify samples (default = "orig.ident").

default_var

logical. Whether to include the default meta.data variables of: "nCount_RNA", "nFeature_RNA", "percent_mito", "percent_ribo", "percent_mito_ribo", and "log10GenesPerUMI" in addition to variables supplied to mad_var.

mad_var

Column(s) in @meta.data to calculate medians for in addition to defaults. Must be of class() integer or numeric.

mad_num

integer value to multiply the MAD in returned data.frame (default is 2). Often helpful when calculating a outlier range to base of of median + (X*MAD).

Examples

if (FALSE) {
mad_stats <- MAD_Stats(seurat_object = obj, group.by = "orig.ident")
}