addReproduciblePeakSet: Add a Reproducible Peak Set to an ArchRProject
In haibol2016/ArchR_debug: Analyzing single-cell regulatory chromatin in R.

addReproduciblePeakSet

R Documentation

Add a Reproducible Peak Set to an ArchRProject

Description

This function will get insertions from coverage files, call peaks, and merge peaks to get a "Union Reproducible Peak Set".

Usage

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"),
  ...
)

Arguments

`ArchRProj`	An `ArchRProject` object.
`groupBy`	The name of the column in `cellColData` to use for grouping cells together for peak calling.
`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 `n` where `n` is the number of samples being assessed. For example, `reproducibility = "2"` means at least 2 samples must have a peak call at this locus and `reproducibility = "(n+1)/2"` means that the majority of samples must have a peak call at this locus.
`peaksPerCell`	The upper limit of the number of peaks that can be identified per cell-grouping in `groupBy`. This is useful for controlling how many peaks can be called from cell groups with low cell numbers.
`maxPeaks`	A numeric threshold for the maximum peaks to retain per group from `groupBy` in the union reproducible peak set.
`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 `seqnames` of the chromosomes that should be excluded from peak calling.
`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` this allows you to create proper fragments, centered at the Tn5 insertion site, for use with MACS2 (see MACS2 documentation).
`extsize`	The number of basepairs to extend the MACS2 fragment after `shift` has been applied. When combined with `extsize` this allows you to create proper fragments, centered at the Tn5 insertion site, for use with MACS2 (see MACS2 documentation).
`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` this gives the method and significance threshold for peak calling (see MACS2 documentation).
`cutOff`	The numeric significance cutOff for the testing method indicated by `method` (see MACS2 documentation).
`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, `extendSummits = 250` will create 501-bp fixed-width peaks from the 1-bp summits.
`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, `promoterRegion = c(2000, 100)` will annotate any peak within the region 2000 bp upstream and 100 bp downstream of a TSS as a "promoter" peak.
`genomeAnnotation`	The genomeAnnotation (see `createGenomeAnnotation()`) to be used for generating peak metadata such as nucleotide information (GC content) or chromosome sizes.
`geneAnnotation`	The geneAnnotation (see `createGeneAnnotation()`) to be used for labeling peaks as "promoter", "exonic", etc.
`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 `ArchRProject` peakSet.
`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 `addGroupCoverages()` to get sample-guided pseudobulk cell-groupings. Only used for TileMatrix-based peak calling (not for MACS2). See `addGroupCoverages()` for more info.