run_comparison: Performs dge, gsea, and GO simplification in one shot for a...
In facilebio/FacileIncubator: Incubator for half-baked ideas

run_comparison

R Documentation

Performs dge, gsea, and GO simplification in one shot for a given analysis.

Description

Performs dge, gsea, and GO simplification in one shot for a given analysis.

Usage

run_comparison(
  params,
  samples = NULL,
  board = pins::board_temp(),
  name = NULL,
  gdb = NULL,
  ffsea_methods = NULL,
  go_ontologies = c("BP", "MF", "CC"),
  go_simplify_method = "ora",
  go_simplify_sem_sim_method = "Resnik",
  go_simplify_max_padj = 0.1,
  go_simplify_sem_threshold = 0.6,
  go_semdata = NULL,
  BPPARAM = BiocParallel::bpparam(),
  direct_dge = NULL,
  ...
)

Arguments

`params`	a list of params used for the analysis. This is typically a single row of a comparison table
`samples`	the facile_frame that includes the sample info
`board`	the pinboard to serialize the results to. If you don't wan to use a fancy remote one, you can always use a local directory.