Quality Control Filter

Removes cells that fail quality control criteria based on marker intensity ranges, cell area, or custom filters.

Usage

qc_filter(
  dt,
  min_area = NULL,
  max_area = NULL,
  min_intensity = 0,
  max_intensity = NULL
)

Arguments

dt

A data.table as returned by read_spatial().

min_area

Numeric or NULL. Minimum cell area. Cells below this threshold are removed.

max_area

Numeric or NULL. Maximum cell area. Cells above this threshold are removed.

min_intensity

Numeric. Minimum total marker intensity. Cells with total intensity below this value are removed. Default 0.

max_intensity

Numeric or NULL. Maximum total marker intensity.

Value

A filtered data.table.

Examples

dt <- data.table::data.table(
  sample_id = "s1", cell_id = 1:10,
  x = runif(10), y = runif(10),
  cell_area = c(5, seq(50, 200, length.out = 8), 5000),
  CD3 = rnorm(10, 300, 50)
)
filtered <- qc_filter(dt, min_area = 10, max_area = 1000)
nrow(filtered)
#> [1] 8