MAD_Stats: Median Absolute Deviation Statistics

In samuel-marsh/scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

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 = "orig.ident",
  default_var = TRUE,
  mad_var = NULL,
  mad_num = 2
)

Arguments

seurat_object	Seurat object name.
group_by_var	Column in meta.data slot to group results by (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).

Value

A data.frame.

Examples

## Not run: 
mad_stats <- MAD_Stats(seurat_object = obj, group_by_var = "orig.ident")

## End(Not run)

samuel-marsh/scCustomize documentation built on Dec. 20, 2024, 7:41 a.m.