remove_var: Remove low variance features from a matrix

In jcalendo/coriell: Convenience Functions for Bioinformatics

Remove low variance features from a matrix

Description

This function removes the p lowest variance features from a matrix. The function expects features in rows and samples in columns (e.g. an expression matrix).

Usage

remove_var(x, ...)

## S3 method for class 'matrix'
remove_var(x, p)

## S3 method for class 'data.frame'
remove_var(x, p)

## S3 method for class 'SummarizedExperiment'
remove_var(x, p, assay = "counts")

Arguments

x	matrix, numeric data.frame, or SummarizedExperiment object
p	proportion of low variance features to remove
assay	if SummarizedExperiment, what assay to use. Default = "counts"

Value

matrix with lowest variance features removed

Examples

# Remove 80% lowest variance features
removed <- remove_var(GSE161650_lc, p = 0.8)

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.