Remove Variables with Low Expression

Filters variables based on median expression values. Variables with median expression values below certain percentile will be removed.

Usage

remove_low_expr(x, percentile = 0.05, by = NULL, strict = FALSE)

Arguments

x

A glyexp::GlycomicSE(), glyexp::GlycoproteomicSE(), or SummarizedExperiment::SummarizedExperiment() object.

percentile

The percentile for median expression values. Defaults to 0.05, i.e., the 5% lowest median expression values will be removed.

by

Either a column name in sample_info (string) or a vector specifying group assignments for each sample.

strict

If FALSE, remove a variable only if it passes the abundance thresholds in all groups. If TRUE, remove a variable if it passes the abundance thresholds in any group. Defaults to FALSE.

Value

A container of the same class as x, with filtered variables.