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Calculate all possible DGE variants (DEPRECATED!)

calculate_all_dges.Rd

This is a deprecated method and will raise an error. Please use calculate_dge_limma() and calculate_dge_hedges().

Usage

calculate_all_dges(
  object,
  contrast_column,
  contrast_list = NULL,
  filter_column = NULL,
  co_variates = NULL,
  small_sample_correction = NULL,
  ...,
  .verbose = TRUE
)

Arguments

object

The underlying class, see BulkDge().

contrast_column

String. The contrast column in which the groupings are stored. Needs to be found in the meta_data within the properties.

contrast_list

Optional string vector. A vectors that contains the contrast formatted as "contrast1-contrast2". Default NULL will create all possible contrast automatically.

filter_column

Optional String. If there is a column you wish to use as sub groupings, this can be provided here. An example could be different sampled tissues and you wish to run the DGE analyses within each tissue separately.

co_variates

Optional string vector. Any co-variates you wish to consider during the Limma Voom modelling.

small_sample_correction

Can be NULL (automatic determination if a small sample size correction should be applied) or a Boolean.

...

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

.verbose

Controls verbosity of the function.

Value

Throws an error, as it is deprecated.