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

In JordanVeldboom/compartmap: A/B compartment inference from ATAC-seq and methylation array data

Description

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

Usage

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

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)
set.seed(1000)
sing_vec <- getSVD(dummy, k = 1, sing.vec = "left")

JordanVeldboom/compartmap documentation built on July 3, 2020, 6:32 p.m.