ElbowCutoff: Elbow Cutoff

In alexthiery/scHelper: R package containing helper functions for single cell analysis

Elbow Cutoff

Description

This function unbiasedly calculates where the principal components start to elbow.

Usage

ElbowCutoff(seurat_object, return = "pc_cutoff")

Arguments

seurat_object	Seurat object
return	either 'pc_cutoff' or 'plot' based on whether the user would like to return a ggplot object or the principle component cutoff point

Details

First we take the larger value of the point where the principal components only contribute 5% of standard deviation and the point where the principal components cumulatively contribute 90% of the standard deviation. Next we take the point where the percent change in variation between the consecutive PCs is less than 0.1%.

The smaller out of these two values is determined at the elbow cutoff

Value

ggplot object OR principle component cutoff

alexthiery/scHelper documentation built on Aug. 26, 2023, 3:42 p.m.