getPeak2GeneLinks.Rd
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 )
ArchRProj | An |
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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 |