addBgdPeaks.Rd
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 |
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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 |