Compute Cohen\'s d for All Gene Signatures Across Conditions

Computes Cohen\'s d effect sizes and corresponding p-values for all gene signatures using scores calculated by various methods. The function first computes gene signature scores using CalculateScores with the "all" option, flattens the results, and then computes pairwise comparisons for a specified grouping variable.

Usage

CohenD_allConditions(
  data,
  metadata,
  gene_sets,
  variable,
  mode = c("simple", "medium", "extensive")
)

Arguments

data

A data frame of gene expression data, with genes as rows and samples as columns.

metadata

A data frame containing sample metadata. The first column should contain sample identifiers matching the column names of data.

gene_sets

A named list of gene sets. For unidirectional gene sets, each element is a vector of gene names; for bidirectional gene sets, each element is a data frame where the first column contains gene names and the second column indicates the expected direction (1 for upregulated, -1 for downregulated).

variable

A string specifying the grouping variable in metadata used to compare scores between conditions.

mode

A string specifying the level of detail for contrasts. Options are:

• "simple": Pairwise comparisons (e.g., A - B).

• "medium": Pairwise comparisons plus comparisons against the mean of other groups.

• "extensive": All possible groupwise contrasts, ensuring balance in the number of terms on each side.

Value

A named list where each element corresponds to a gene signature. Each signature element is a list with three components:

CohenD

A data frame where rows are methods and columns are group contrasts (formatted as \"Group1:Group2\"), containing the computed Cohen\'s d effect sizes.

PValue

A data frame with the same structure as CohenD containing the corresponding p-values.

padj

A data frame with the same structure as PValue containing the corresponding p-values corrected using the BH method, for all signatures and contrasts, and by method.

Examples

if (FALSE) { # \dontrun{
  # Assume gene_data is your gene expression data frame, sample_metadata is your metadata, and
  # gene_sets is a named list of gene sets.
  results <- CohenD_allConditions(data = gene_data, metadata = sample_metadata,
                                  gene_sets = gene_sets, variable = "Condition")
  # Access Cohen's d for a specific signature:
  results$Signature_A$CohenD
} # }