extractOpenClosed: Get the open and closed compartment calls based on sign of...

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

Get the open and closed compartment calls based on sign of singular values

Description

Get the open and closed compartment calls based on sign of singular values

Usage

extractOpenClosed(gr, cutoff = 0, assay = c("rna", "atac", "array"))

Arguments

gr	Input GRanges with associated mcols that represent singular values
cutoff	Threshold to define open and closed states
assay	The type of assay we are working with

Value

A vector of binary/categorical compartment states

Examples

dummy <- matrix(rnorm(10000), ncol=25)
sing_vec <- getSVD(dummy, k = 1, sing.vec = "right")

biobenkj/compartmentalizer documentation built on Oct. 13, 2023, 5:26 p.m.