View source: R/ReproduciblePeakSet.R
addReproduciblePeakSet | R Documentation |
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). This is required if genome is not hg19, hg38, mm9, or mm10. |
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 |
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