Skip to contents

Rescue MAD-flagged cells that fall within safe bounds

rescue_cells.Rd

For each metric in rescue_thresholds, cells whose value is within [lower, upper] are un-flagged from MAD. Hard-threshold flags are not cleared; a warning is issued when overlaps occur. Calling rescue_cells overwrites any prior rescue set for the metrics named.

Usage

rescue_cells(x, rescue_thresholds)

Arguments

x

A CellQc object.

rescue_thresholds

Named list of numeric vectors with lower and/or upper.

Value

Updated CellQc.

Examples

# un-flag MAD outliers that still sit above a sane library size
set.seed(42L)
metrics <- list(
  lib_size = c(rnorm(99, 1000, 100), 50),
  pct_mt = runif(100, 0, 20)
)
qc <- run_cell_qc(
  metrics,
  cells_to_keep = 0:99,
  directions = c(lib_size = "below", pct_mt = "above")
)
rescue_cells(qc, list(lib_size = c(lower = 500)))
#> CellQc: 100 cells, 1 outliers (1.0%)
#> Metrics:
#>   - lib_size: 1 outliers (mad = 5, rescued = 4)
#>     MAD lower = 816.05
#>   - pct_mt: 0 outliers (mad = 0)
#>     MAD upper = 23.60