Rank normalization methods by median PMAD (ascending – lower is better) — nm_rank_pmad • NADIA

Rank normalization methods by median PMAD (ascending – lower is better)

Usage

nm_rank_pmad(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  verbose = TRUE
)

Arguments

se: SummarizedExperiment from import_norm_matrices().
assay_names: Character vector of assay names to include. NULL = all.
condition_col: Column in colData with condition labels.
verbose: Logical. Print progress messages. Default TRUE.

Value

A data.frame with columns Method, Median_PMAD, Rank.

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
se <- nm_run_normalizations(se, methods = c("cycloess", "quantile", "MAD"),
                            verbose = FALSE)

nm_rank_pmad(se, verbose = FALSE)
#>     Method Median_PMAD Rank
#> 1 cycloess  0.06634680    1
#> 2 quantile  0.06851739    2
#> 3      MAD  0.07282100    3
#> 4     log2  0.17211589    4