Get the peak-to-gene links from an ArchRProject

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

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().