Export Group BigWigs

This function will group, summarize and export a bigwig for each group in an ArchRProject.

getGroupBW(
  ArchRProj = NULL,
  groupBy = "Sample",
  normMethod = "ReadsInTSS",
  tileSize = 100,
  maxCells = 1000,
  ceiling = 4,
  verbose = TRUE,
  threads = getArchRThreads(),
  logFile = createLogFile("getGroupBW")
)

Arguments

ArchRProj

An ArchRProject object.

groupBy

A string that indicates how cells should be grouped. This string corresponds to one of the standard or user-supplied cellColData metadata columns (for example, "Clusters"). Cells with the same value annotated in this metadata column will be grouped together and the average signal will be plotted.

normMethod

The name of the column in cellColData by which normalization should be performed. The recommended and default value is "ReadsInTSS" which simultaneously normalizes tracks based on sequencing depth and sample data quality.

tileSize

The numeric width of the tile/bin in basepairs for plotting ATAC-seq signal tracks. All insertions in a single bin will be summed.

maxCells

Maximum number of cells used for each bigwig.

ceiling

Maximum contribution of accessibility per cell in each tile.

verbose

A boolean specifying to print messages during computation.

threads

An integer specifying the number of threads for parallel.

logFile

The path to a file to be used for logging ArchR output.