getPeak2GeneLinks | R Documentation |
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 |
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 |
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