Top_Genes_Factor: Extract top loading genes for LIGER factor

In scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Extract top loading genes for LIGER factor

Description

Extract vector to the top loading genes for specified LIGER iNMF factor

Usage

Top_Genes_Factor(object, factor = NULL, num_genes = 10, ...)

## S3 method for class 'liger'
Top_Genes_Factor(object, factor = NULL, num_genes = 10, ...)

## S3 method for class 'Seurat'
Top_Genes_Factor(object, factor = NULL, num_genes = 10, reduction, ...)

Arguments

object	object name.
factor	factor number to pull genes from. Set to "all" to return top loading genes from all factors
num_genes	number of top loading genes to return as vector, default is 10.
...	Arguments passed to other methods
reduction	name of reduction containing NMF/iNMF/cNMF data.

Value

vector of top genes for given factor or data.frame containing top genes across all factors

Examples

## Not run: 
top_genes_factor10 <- Top_Genes_Factor(object = object, factor = 1, num_genes = 10)

## End(Not run)

## Not run: 
top_genes_factor10 <- Top_Genes_Factor(object = object, factor = 1, num_genes = 10,
reduction = "cNMF")

## End(Not run)

scCustomize documentation built on Aug. 26, 2025, 9:08 a.m.