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Run differential expression on all studies

Source: R/03_de.R
mx_de_all.Rd

Applies mx_de to each study in a list, optionally in parallel using BiocParallel.

Usage

mx_de_all(
  studies,
  method = "DESeq2",
  formula = ~condition,
  contrast = NULL,
  BPPARAM = BiocParallel::SerialParam(),
  ...
)

Arguments

studies

A named list of metaXpressStudy objects.

method

Character scalar. DE method passed to mx_de. Default: "DESeq2".

formula

A design formula (see mx_de), or a list of formulas with one entry per study when covariates differ between studies. Default: ~ condition.

contrast

NULL, a length-2 character vector c(case, control) applied to every study, or a list with one such vector per study (labels often differ between GEO series).

BPPARAM

A BiocParallelParam object controlling parallelization. Defaults to SerialParam() (single-core). Use MulticoreParam() for multi-core execution.

...

Additional arguments passed to mx_de.

Value

The input list of studies, each with de_result slot filled.

See also

mx_de, mx_de_summary

Examples

if (FALSE) { # \dontrun{
  studies <- mx_de_all(studies, method = "DESeq2")
  # Parallel:
  studies <- mx_de_all(studies, method = "DESeq2",
                        BPPARAM = BiocParallel::MulticoreParam(4))
} # }