Rank normalization methods by median intragroup correlation (descending – higher is better) — nm_rank_cor • NADIA

Rank normalization methods by median intragroup correlation (descending – higher is better)

Usage

nm_rank_cor(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  cor_method = "pearson",
  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.
cor_method: Correlation method: "pearson", "spearman", or "kendall".
verbose: Logical. Print progress messages. Default TRUE.

Value

A data.frame with columns Method, Median_Cor, 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_cor(se, cor_method = "pearson", verbose = FALSE)
#>     Method Median_Cor Rank
#> 1 cycloess  0.9866091    1
#> 2     log2  0.9865677    2
#> 3      MAD  0.9865677    3
#> 4 quantile  0.9864951    4