addBgdPeaks | R Documentation |
This function will compute background peaks controlling for total accessibility and GC-content and add this information to an ArchRProject.
addBgdPeaks(
ArchRProj = NULL,
nIterations = 50,
w = 0.1,
binSize = 50,
seed = 1,
method = "chromVAR",
outFile = file.path(getOutputDirectory(ArchRProj), "Background-Peaks.rds"),
force = FALSE
)
ArchRProj |
An |
nIterations |
The number of background peaks to sample. See |
w |
The parameter controlling similarity of background peaks. See |
binSize |
The precision with which the similarity is computed. See |
seed |
A number to be used as the seed for random number generation. It is recommended to keep track of the seed used so that you can reproduce results downstream. |
method |
A string indicating whether to use chromVAR or ArchR for background peak identification. |
outFile |
The path to save the |
force |
A boolean value indicating whether to force the file indicated by |
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