labelBulk: Label bulk data

In PFPrzytycki/CellWalkR: An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

Label bulk data

Description

labelBulk() Determines labels for bulk data by mapping them via the calculated information matrix

Usage

labelBulk(
  cellWalk,
  bulkPeaks,
  ATACMat,
  peaks,
  extendRegion,
  extendDistance,
  cellTypes,
  allScores = FALSE,
  parallel = FALSE,
  numCores = 1
)

Arguments

cellWalk	a cellWalk object
bulkPeaks	GRanges of peaks in bulk data or GRangesList of sets of peaks
ATACMat	cell-by-peak matrix
peaks	GRanges of peaks in ATACMat
extendRegion	GRanges defining where to extend mapping to consider peaks in a larger region (e.g. in LD) with bulk data
extendDistance	numeric maximum distance to extend region by (if region is missing, just distance is used, if distance is missing whole region is used)
cellTypes	character, vector of labels to use, all labels used by default
allScores	return full table of scores
parallel	execute in parallel
numCores	number of cores to use for parallel execution

Value

labels for each region in bulk data

Examples

data("SampleCellWalkRData")
labelBulk(SampleCellWalkRData$cellWalk,
          SampleCellWalkRData$sampleEnhancers,
          SampleCellWalkRData$ATACMat,
          SampleCellWalkRData$peaks)

PFPrzytycki/CellWalkR documentation built on Oct. 26, 2023, 1:50 p.m.