Calculate marker expression purity for each cell given a marker list

Calculate marker expression purity for each cell given a marker list

calMarkerPct(
  spe,
  celltype,
  marker_list,
  marker_list_name = "",
  exprs_values = "logcounts",
  threshold = 0,
  use_BPPARAM = BiocParallel::SerialParam()
)

Arguments

spe

A Spatial Experiment object

celltype

A string or a vector indicating the cell type information. If it is a string, it will retrive the information from colData.

marker_list

A list of marker, the name of the list corresponding to the cell type information provided in `celltype`.

marker_list_name

A string specifying the name to be used to store the result.

exprs_values

A string indicating which assay of `spe` contains the expression values.

threshold

A numeric indicating the threshold to be considered as expressed.

use_BPPARAM

A BiocParallelParam instance determining the parallel back-end to be used during evaluation.

Value

A SpatialExperiment object