computeLabelEdges: Compute Label Edges

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

Compute Label Edges

Description

computeLabelEdges generates a matrix of edges from each label to each cell. Edges are scaled by the passed weights and filters. Each filter can either apply just to specific peaks or to whole genes (filterGene, TRUE by default) and can be permissive or filtering out (filterOut, FALSE by default). Regions mapping peaks to genes must be provided to use filters. If filters are applied to specific peaks, peaks for the ATAC data must also be provided.

Usage

computeLabelEdges(
  labelGenes,
  ATACMat,
  ATACGenePeak,
  method = "Expression",
  filters,
  filterWeights,
  filterOut,
  filterGene,
  regions,
  peaks,
  whichMat = "bmat"
)

Arguments

labelGenes	data.frame with genes of interest in first column and corresponding labels in second column, optionally log-fold change in expression values in the third
ATACMat	either a cell-by-peak matrix, a SnapATAC object, or an ArchR project
ATACGenePeak	per label mapping of peaks to genes returned by mapPeaksToGenes()
method	scaling method, either "Expression","Correlation", or "None"
filters	list of GRanges lists for locations that pass filters
filterWeights	numeric vector of weights assigned to each filter
filterOut	boolean for each filter of whether those regions are permitted or filtered out
filterGene	boolean for each filter of whether it applies to genes as a whole or just overlapping peaks (note that weights do not apply to peaks)
regions	regions map peaks to genes
peaks	GRanges of peaks in ATACMat
whichMat	string determing whether to use "bmat" or "gmat" from snap object or "TileMatrix" or "GeneScoreMatrix" from ArchR project

Value

matrix of weights from each label to each cell

Examples

data("SampleCellWalkRData")
computeLabelEdges(SampleCellWalkRData$labelGenes,
                  SampleCellWalkRData$ATACMat,
                  SampleCellWalkRData$ATACGenePeak)

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