addAccessibilityShift: 'addAccessibilityShift'

In MOCHA: Modeling for Single-Cell Open Chromatin Analysis

addAccessibilityShift

Description

addAccessibilityShift will add a new condition to the SummarizedExperiment output of extractRegion, which will contain the difference in accessibility between two conditions

Usage

addAccessibilityShift(CountSE, foreground, background, assayName = NULL)

Arguments

CountSE	The SummarizedExperiment object output from extractRegion
foreground	Group that will be used as the foreground for the subtraction of accessibility
background	Group that will be used as the background for the subtraction of accessibility
assayName	The name given to the new assay that is difference in accessibility between foreground and background.

Value

countSE a SummarizedExperiment containing coverage for the given input cell populations.

Examples

## Not run: 
# CountSE is a SummarizedExperiment generated by extractRegion()
countSE <- MOCHA::addAccessibilityShift(
  CountSE = CountSE,
  foreground = "Condition1",
  background = "Condition2",
  assayName = "AccessibilityChanges"
)

## End(Not run)

MOCHA documentation built on May 29, 2024, 2:25 a.m.