select_hvgs: Select highly variable genes (HVGs)

In byzhang23/TreeCorTreat: Tree-based correlation screen for phenotype-associated transcriptomic features and cell types

Select highly variable genes (HVGs)

Description

This function takes in normalized sample-level pseudobulk as input and identifies highly variable genes.

Usage

select_hvgs(expr, num_hvgs = NULL)

Arguments

expr

Sample-level pseudobulk gene expression matrix

num_hvgs

Number of highly variable genes extracted from sample-level pseudobulk. Highly variable genes (HVGs) are defined as genes with positive residuals by fitting a gene-specific lowess (loessFit) function of standard deviation against its mean. The HVGs are ordered by residuals in a descending order. Default is NULL, which includes all genes with positive residuals. Can specify a reasonable positive number (e.g. 1000).

Value

A vector of highly variable gene names

Author(s)

Boyang Zhang <[e-mail]>, Hongkai Ji

byzhang23/TreeCorTreat documentation built on May 7, 2024, 8:37 a.m.