getSampleTileMatrix {MOCHA}

getSampleTileMatrix

Description

getSampleTileMatrix takes the output of peak calling with callOpenTiles and creates sample-tile matrices containing the signal intensity at each tile.

Usage

getSampleTileMatrix(
  tileResults,
  cellPopulations = "ALL",
  groupColumn = NULL,
  threshold = 0.2,
  numCores = 1,
  verbose = FALSE
)

Arguments

tileResults

a MultiAssayExperiment returned by callOpenTiles containing containing peak calling results.

cellPopulations

vector of strings. Cell subsets in TileResults for which to generate sample-tile matrices. This list of group names must be identical to names that appear in the ArchRProject metadata. If cellPopulations='ALL', then peak calling is done on all cell populations in the ArchR project metadata. Default is 'ALL'.

groupColumn

Optional, the column containing sample group labels for determining consensus tiles within sample groups. Default is NULL, all samples will be used for determining consensus tiles.

threshold

Threshold for consensus tiles, the minimum % of samples (within a sample group, if groupColumn is set) that a peak must be called in to be retained. If set to 0, retain the union of all samples' peaks (this is equivalent to a threshold of 1/numSamples). It is recommended to tune this parameter to omit potentially spurious peaks.

numCores

Optional, the number of cores to use with multiprocessing. Default is 1.

verbose

Set TRUE to display additional messages. Default is FALSE.

Value

SampleTileMatrices a MultiAssayExperiment containing a sample-tile intensity matrix for each cell population

Examples

# Starting from GRangesList
if (
  require(BSgenome.Hsapiens.UCSC.hg19) &&
    require(TxDb.Hsapiens.UCSC.hg38.refGene) &&
    require(org.Hs.eg.db)
) {
  tiles <- MOCHA::callOpenTiles(
    ATACFragments = MOCHA::exampleFragments,
    cellColData = MOCHA::exampleCellColData,
    blackList = MOCHA::exampleBlackList,
    genome = "BSgenome.Hsapiens.UCSC.hg19",
    TxDb = "TxDb.Hsapiens.UCSC.hg38.refGene",
    Org = "org.Hs.eg.db",
    outDir = tempdir(),
    cellPopLabel = "Clusters",
    cellPopulations = c("C2", "C5"),
    numCores = 1
  )

  SampleTileMatrices <- MOCHA::getSampleTileMatrix(
    tiles,
    cellPopulations = c("C2", "C5"),
    threshold = 0 # Take union of all samples' open tiles
  )
}