Materialize expensive carnation object components

This function materializes expensive derived pieces for a validated carnation object, including DESeqDataSet creation from raw count matrices, variance-stabilized counts, and GeneTonic conversions.

Usage

materialize_carnation_object(obj, config = NULL, cores = NULL)

Arguments

obj

A validated object returned by validate_carnation_object() or validate_loaded_carnation_object().

config

Optional config list. If NULL, will use get_config().

cores

Optional number of worker processes. If NULL, uses config$server$cores.

Value

The input object with materialized dds_list, rld_list, and optional genetonic slots.

Examples

if (FALSE) { # interactive()
# Minimal example with DE results and counts
library(DESeq2)

# Create example data
dds <- makeExampleDESeqDataSet()
dds <- DESeq(dds)
res <- results(dds, contrast = c("condition", "A", "B"))
rld <- varianceStabilizingTransformation(dds, blind = TRUE)

# Validate object inputs
obj <- validate_carnation_object(
  res_list = list(
    comp1 = list(
      res = as.data.frame(res),
      dds = "main",
      label = "A vs B"
    )
  ),
  dds_list = list(main = dds),
  rld_list = list(main = rld)
)

materialized <- materialize_carnation_object(obj, cores = 1)
}