addReproduciblePeakSet.Rd
This function will get insertions from coverage files, call peaks, and merge peaks to get a "Union Reproducible Peak Set".
addReproduciblePeakSet( ArchRProj = NULL, groupBy = "Clusters", peakMethod = "Macs2", reproducibility = "2", peaksPerCell = 500, maxPeaks = 150000, minCells = 25, excludeChr = c("chrM", "chrY"), pathToMacs2 = if (tolower(peakMethod) == "macs2") findMacs2() else NULL, genomeSize = NULL, shift = -75, extsize = 150, method = if (tolower(peakMethod) == "macs2") "q" else "p", cutOff = 0.1, additionalParams = "--nomodel --nolambda", extendSummits = 250, promoterRegion = c(2000, 100), genomeAnnotation = getGenomeAnnotation(ArchRProj), geneAnnotation = getGeneAnnotation(ArchRProj), plot = TRUE, threads = getArchRThreads(), parallelParam = NULL, force = FALSE, verbose = TRUE, logFile = createLogFile("addReproduciblePeakSet"), ... )
ArchRProj | An |
---|---|
groupBy | The name of the column in |
peakMethod | The name of peak calling method to be used. Options include "Macs2" for using macs2 callpeak or "Tiles" for using a TileMatrix. |
reproducibility | A string that indicates how peak reproducibility should be handled. This string is dynamic and can be a
function of |
peaksPerCell | The upper limit of the number of peaks that can be identified per cell-grouping in |
maxPeaks | A numeric threshold for the maximum peaks to retain per group from |
minCells | The minimum allowable number of unique cells that was used to create the coverage files on which peaks are called. This is important to allow for exclusion of pseudo-bulk replicates derived from very low cell numbers. |
excludeChr | A character vector containing the |
pathToMacs2 | The full path to the MACS2 executable. |
genomeSize | The genome size to be used for MACS2 peak calling (see MACS2 documentation). |
shift | The number of basepairs to shift each Tn5 insertion. When combined with |
extsize | The number of basepairs to extend the MACS2 fragment after |
method | The method to use for significance testing in MACS2. Options are "p" for p-value and "q" for q-value. When combined with
|
cutOff | The numeric significance cutOff for the testing method indicated by |
additionalParams | A string of additional parameters to pass to MACS2 (see MACS2 documentation). |
extendSummits | The number of basepairs to extend peak summits (in both directions) to obtain final fixed-width peaks. For example,
|
promoterRegion | A vector of two integers specifying the distance in basepairs upstream and downstream of a TSS to be included as a promoter region.
Peaks called within one of these regions will be annotated as a "promoter" peak. For example, |
genomeAnnotation | The genomeAnnotation (see |
geneAnnotation | The geneAnnotation (see |
plot | A boolean describing whether to plot peak annotation results. |
threads | The number of threads to be used for parallel computing. |
parallelParam | A list of parameters to be passed for biocparallel/batchtools parallel computing. |
force | A boolean value indicating whether to force the reproducible peak set to be overwritten if it already exist in the given |
verbose | A boolean value that determines whether standard output includes verbose sections. |
logFile | The path to a file to be used for logging ArchR output. |
... | Additional parameters to be pass to |