Parallel processing handling function

Boot_parallel(
  BPPARAM = NULL,
  samples,
  data,
  formula.str,
  group,
  groups,
  meta.info,
  a1,
  a2,
  pSamples,
  correlation_block = NULL
)

Arguments

BPPARAM: A parallel BPPARAM object for distributed computation.
samples: bootstrapped samples matrix
data: A SummarizedExperiment object or a matrix where rows represent features (e.g., genes, proteins) and columns represent samples. The values should be log-transformed.
formula.str: A formula string used when covariates are present in meta. info for modeling. It should include "~ 0 + ..." to exclude the intercept from the model.
group: A string specifying the column in meta.info that represents the groups or conditions for comparison.
groups: groups information from meta.info
meta.info: A data frame containing sample-level metadata, where each row corresponds to a sample. It should include the grouping variable specified in group. If x is a SummarizedExperiment object, meta.info must be a vector of the metadata needed for the model to run and can be retrieved using colData().
a1: Optional numeric value used in the optimization process. If defined by the user, no optimization occurs.
a2: Optional numeric value used in the optimization process. If defined by the user, no optimization occurs.
pSamples: a permutated list of samples
correlation_block: Character or NULL. The name of a column in meta.info that defines correlation blocks. Passed to Limma_bootstrap and Limma_permutating to account for within-block correlation during model fitting via duplicateCorrelation. If NULL, standard independent fitting is used.

Value

A list containing: D, S, pD, pS for bootstrapped data and for permuted data.