View source: R/MatrixDeviations.R
addDeviationsMatrix | R Documentation |
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 |
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. |
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