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Wrapper for a Limma Voom analysis

run_limma_voom.Rd

Wrapper function to run Limma Voom workflows.

Usage

run_limma_voom(
  meta_data,
  main_contrast,
  dge_list,
  contrast_list = NULL,
  co_variates = NULL,
  quantile_norm = FALSE,
  ...,
  .verbose = TRUE
)

Arguments

meta_data

data.table. The meta information about the experiment in which the contrast info (and potential co-variates) can be found.

main_contrast

String. Which column contains the main groups you want to test differential gene expression with the Limma-Voom workflow for.

dge_list

DGEList, see edgeR::DGEList().

contrast_list

String vector or NULL. Optional string vector of contrast formatted as "contrast1-contrast2". Default NULL will create all contrasts automatically.

co_variates

String or NULL. Optional co-variates you wish to consider during model fitting.

quantile_norm

Boolean. Shall the counts be also quantile-normalised. Defaults to FALSE.

...

Additional parameters to forward to limma::eBayes() or limma::voom().

.verbose

Boolean. Controls verbosity of the function.

Value

A data.table with all the DGE results from limma::topTable() for the identified contrast pairs.