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. If this value is positive, then only positive correlations greater than or equal to corCutOff will be returned. If this value is negative, then only negative correlations less than or equal to corCutOff will be returned. If corCutOff = 0, only positive correlations will be returned.

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().

Examples

# Get Test ArchR Project
proj <- getTestProject()

# Add P2G Links
proj <- addPeak2GeneLinks(proj, k = 20)

# Get P2G Links
p2g <- getPeak2GeneLinks(proj)