cleanAssayRows: Remove rows with NAs exceeding a threshold

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

Remove rows with NAs exceeding a threshold

Description

Remove rows with NAs exceeding a threshold

Usage

cleanAssayRows(se, rowmax = 0.5, assay = c("array", "bisulfite"))

Arguments

se	Input SummarizedExperiment object
rowmax	The maximum NAs allowed in a row as a fraction
assay	The type of assay we are working with

Value

A filtered matrix

Examples

if (require(minfi)) {
  data("meth_array_450k_chr14", package = "compartmap")
  cleanAssayRows(array.data.chr14, assay = "array")
}

biobenkj/compartmap documentation built on Feb. 21, 2025, 9:14 p.m.