step_select_genes: Gene selection by differential expression analysis.
In mirvie/mirmodels: Models Built by the Informatics Team at Mirvie

step_select_genes() creates a specification of a recipe step that will select genes by differential expression analysis, discarding those that don't pass a certain p-value threshold. Currently, cor_de() is used.

step_select_genes(
  recipe,
  ...,
  role = NA,
  trained = FALSE,
  condition = NULL,
  genes_pass = NULL,
  padj_cutoff = 0.05,
  max_n_genes = NULL,
  min_n_genes = NULL,
  options = list(method = "spearman", padj_method = stats::p.adjust.methods[1]),
  skip = FALSE,
  id = recipes::rand_id("select_genes")
)

`recipe`	A recipe object. The step will be added to the sequence of operations for this recipe.
`...`	One or more selector functions to choose which variables will be used to compute the components. See `selections()` for more details. For the `tidy` method, these are not currently used.
`role`	For model terms created by this step, what analysis role should they be assigned?. By default, the function assumes that the new principal component columns created by the original variables will be used as predictors in a model.
`trained`	A logical to indicate if the quantities for preprocessing have been estimated.
`condition`	The condition for the differential expression. See `cor_de()`.
`genes_pass`	This should not be specified by the end user. Information about which genes do and don't pass the p-value threshold in the differential expression analysis is stored here.
`padj_cutoff`	Genes with an adjusted p-value less than or equal to `padj_cutoff` in the differential expression analysis are kept. The rest are discarded.
`max_n_genes`	A positive integer. The maximum number of genes selected by this step.
`min_n_genes`	A positive integer. The minimum number of genes selected. This guarantees that even if no genes pass `padj_cutoff`, there will be this many returned.
`options`	A list with two elements named `method` and `padj_method`. Both are passed to `cor_de()`. `padj_cutoff` is the threshold for keeping genes.
`skip`	A logical. Should the step be skipped when the recipe is baked by `bake.recipe()`? While all operations are baked when `prep.recipe()` is run, some operations may not be able to be conducted on new data (e.g. processing the outcome variable(s)). Care should be taken when using `skip = TRUE` as it may affect the computations for subsequent operations
`id`	A character string that is unique to this step to identify it.