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A report of flagged features

Source: R/transformations.R
flag_report.Rd

Computes the number of features at each stage of flagging for each mode.

Usage

flag_report(object)

Arguments

object

a SummarizedExperiment object

Value

A data frame with the number of features at each stage of flagging.

Examples

data(toy_notame_set)
flagged <- toy_notame_set |>
  mark_nas(0) |>
  flag_detection(group = "Group") |>
  flag_quality()
#> INFO [2025-10-29 12:02:59] 
#> 1% of features flagged for low detection rate
#> INFO [2025-10-29 12:02:59] 
#> 91% of features flagged for low quality
flag_report(flagged)
#>       Split Kept Low_quality Total Flagged Low_qc_detection
#> 1 HILIC_neg    3          17    20      17               NA
#> 2 HILIC_pos    1          18    20      19                1
#> 3    RP_neg    2          18    20      18               NA
#> 4    RP_pos    0          20    20      20               NA