getCoAccessibility: Get the peak co-accessibility from an ArchRProject
In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

getCoAccessibility

R Documentation

Get the peak co-accessibility from an ArchRProject

Description

This function obtains co-accessibility data from an ArchRProject.

Usage

getCoAccessibility(
  ArchRProj = NULL,
  corCutOff = 0.5,
  resolution = 1,
  returnLoops = TRUE
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`corCutOff`	A numeric describing the minimum numeric peak-to-peak correlation to return.
`resolution`	A numeric describing the bp resolution to use when returning loops. This helps with overplotting of correlated regions. This only takes affect if `returnLoops = TRUE`.
`returnLoops`	A boolean indicating to return the co-accessibility signal as a `GRanges` "loops" object designed for use with the `ArchRBrowser()` or as an `ArchRBrowserTrack()`.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Add Co Accessibility
proj <- addCoAccessibility(proj, k = 20)

# Get Co Accessibility
CoA <- getCoAccessibility(proj)

GreenleafLab/ArchR documentation built on Feb. 21, 2025, 3:05 p.m.