cleanAssayCols: Remove columns/cells/samples with NAs exceeding a threshold....

In biobenkj/compartmentalizer: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Remove columns/cells/samples with NAs exceeding a threshold. See cleanAssay()

Description

Remove columns/cells/samples with NAs exceeding a threshold. See cleanAssay()

Usage

cleanAssayCols(se, na.max = 0.8, assay = c("array", "bisulfite"))

Arguments

se	Input SummarizedExperiment object
na.max	The maximum number of NAs allowed as a fraction
assay	The type of assay we are working with

Value

A filtered matrix

Examples

if (requireNamespace("minfi", quietly = TRUE)) {
  data("array_data_chr14", package = "compartmap")
  compartmap:::cleanAssayCols(array.data.chr14, assay = "array")
}

biobenkj/compartmentalizer documentation built on June 10, 2025, 1:57 a.m.