qc_metrics — qc_metrics • SpatialMap

calculates QC metrics from Region object

Usage

qc_metrics(
  object,
  slot = "Data",
  DNA = "DAPI",
  cell.size = "size",
  summary.fun = "mean",
  markers = NULL
)

object: A Region object
slot: The data slot to pull data on markers from.
DNA: The feature name of the DNA channel. Must be found in the bgData slot.
cell.size: The feature name of the cell size parameter. Must be found in the coords or cellMetadata slot.
summary.fun: If there are multiple channels that match the DNA argument (for example, multiple DAPI channels), choose how to summarize them. Defaults to "mean".
markers: Specific markers to run qc metrics on (character vector). Impacts the calculation of signal.sum and signal.CV. Must specify more than one marker. Default NULL will run all.