getPeak2GeneLinks: Get the peak-to-gene links from an ArchRProject

In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

Get the peak-to-gene links from an ArchRProject

Description

This function obtains peak-to-gene links from an ArchRProject.

Usage

getPeak2GeneLinks(
  ArchRProj = NULL,
  corCutOff = 0.45,
  FDRCutOff = 1e-04,
  varCutOffATAC = 0.25,
  varCutOffRNA = 0.25,
  resolution = 1,
  returnLoops = TRUE
)

Arguments

ArchRProj	An ArchRProject object.
corCutOff	A numeric describing the minimum numeric peak-to-gene correlation to return.
FDRCutOff	A numeric describing the maximum numeric peak-to-gene false discovery rate to return.
varCutOffATAC	A numeric describing the minimum variance quantile of the ATAC peak accessibility when selecting links.
varCutOffRNA	A numeric describing the minimum variance quantile of the RNA gene expression when selecting links.
resolution	A numeric describing the bp resolution to return loops as. This helps with overplotting of correlated regions.
returnLoops	A boolean indicating to return the peak-to-gene links as a GRanges "loops" object designed for use with the ArchRBrowser() or as an ArchRBrowserTrack().

haibol2016/ArchR_debug documentation built on June 15, 2022, 5:42 p.m.