addDeviationsMatrix.Rd
This function will compute peakAnnotation deviations for each ArrowFiles independently while controlling for global biases (low-memory requirement).
addDeviationsMatrix( ArchRProj = NULL, peakAnnotation = NULL, matches = NULL, bgdPeaks = getBgdPeaks(ArchRProj, method = "chromVAR"), matrixName = NULL, out = c("z", "deviations"), binarize = FALSE, threads = getArchRThreads(), verbose = TRUE, parallelParam = NULL, force = FALSE, logFile = createLogFile("addDeviationsMatrix") )
ArchRProj | An |
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peakAnnotation | The name of the |
matches | A custom |
bgdPeaks | A |
matrixName | The name to be used for storage of the deviations matrix in the provided |
out | A string or character vector that indicates whether to save the ouptut matrices as deviations ("deviations") z-scores ("z"), or both (c("deviations","z")). |
binarize | A boolean value indicating whether the input matrix should be binarized before calculating deviations. This is often desired when working with insertion counts. |
threads | The number of threads to be used for parallel computing. |
verbose | A boolean value that determines whether standard output includes verbose sections. |
parallelParam | A list of parameters to be passed for biocparallel/batchtools parallel computing. |
force | A boolean value indicating whether to force the matrix indicated by |
logFile | The path to a file to be used for logging ArchR output. |