ChoosePCs: Automatically choose the number of principal components.

In jr-leary7/SCISSORS: Identify cell subpopulations in single cell RNA-seq data

Automatically choose the number of principal components.

Description

This function uses the eigenvalues of the principal component matrix to determine the best number of PCs. The default can be chosen automatically, or given by the user. It is intended to be run after RunPCA.

Usage

ChoosePCs(seurat.obj = NULL, cutoff = 0.15)

Arguments

seurat.obj	The object containing our single cell counts and principal component matrix. Defaults to NULL.
cutoff	The cutoff value for cumulative proportion of variance explained. Can be set by the user, or can be determine automatically. Defaults to 15%.

Value

An integer specifying the number of PCs to use.

Author(s)

Jack Leary

Examples

## Not run: 
ChoosePCs(seurat.obj = pbmc, cutoff = .3)

## End(Not run)

jr-leary7/SCISSORS documentation built on April 20, 2023, 8:21 p.m.