adjust_pval: Adjust P-values in a `dana` object

Description

Applies multiple testing correction to P-values from differential analysis results returned by the dana() function. Supports multiple adjustment methods and both coefficient and likelihood ratio test (LRT) P-values.

Usage

adjust_pval(
  dana_obj,
  padj_by = c("all", "terms"),
  padj_method = c("BH", "bonferroni", "BY", "fdr", "hochberg", "holm", "hommel", "IHW",
    "storey"),
  padj_method_LRT = c("BH", "bonferroni", "BY", "fdr", "hochberg", "holm", "hommel",
    "IHW", "storey"),
  verbose = TRUE,
  ...
)

Value

A modified dana object with new columns in the $fit and $lrt data frames for each adjusted P-value method applied (e.g. padj_BH, padj_storey_group).

Arguments

dana_obj: A dana class object returned by the dana() function.
padj_by: Character string. Whether P-value adjustment should be done globally across all coefficients ("all") or separately for each coefficient term ("terms").
padj_method: Character vector of one or more methods for adjusting P-values from coefficient tests. Defaults to "BH".
padj_method_LRT: Character vector of one or more methods for adjusting P-values from LRT tests. Defaults to "BH". P-values from LRT tests will always be adjusted independently for each LRT term.
verbose: Logical. Whether to print informative messages. Defaults to TRUE.
...: Additional arguments passed to IHW::ihw() or qvalue::qvalue().

Details

Available adjustment methods include: "BH", "bonferroni", "BY", "fdr", "hochberg", "holm", "hommel", "IHW", and "storey".

Examples

Run this code

set.seed(123)
mock_X <- matrix(rnorm(20 * 5), nrow = 20)
colnames(mock_X) <- paste0("feat_", seq_len(5))
rownames(mock_X) <- paste0("sample_", seq_len(20))

sample_data <- data.frame(
  sample_id = rownames(mock_X),
  group = factor(rep(c("A", "B"), each = 10)),
  time = factor(rep(c("T1", "T2"), times = 10)),
  subject_id = factor(rep(seq_len(10), each = 2)),
  stringsAsFactors = FALSE
)
rownames(sample_data) <- sample_data$sample_id

fit_df <- data.frame(
  feat_id = rep(colnames(mock_X), each = 2),
  Coefficient = rep(c("(Intercept)", "groupB"), 5),
  Estimate = rnorm(10),
  `Pr(>|t|)` = runif(10),
  stringsAsFactors = FALSE
)

# Mock dana object
dana_obj <- list(
  X = mock_X,
  sdata = sample_data,
  formula_rhs = ~ group,
  fit = fit_df,
  lrt = data.frame(),
  ranef = data.frame()
)
class(dana_obj) <- "dana"

# Add adjusted P-values
dana_obj <- dana_obj |>
  adjust_pval(dana_obj,
              padj_method = c("BH", "bonferroni"),
              padj_method_LRT = NULL,
              padj_by = "terms",
              verbose = FALSE)