create a module based on provided sample sets

create a module based on provided sample sets

create_module_ss(
  compendium = "vespucci",
  samplesetNames = NULL,
  normalization = "limma",
  rank = "uncentered_correlation",
  top_n = 50,
  sorted = FALSE,
  useIds = FALSE
)

Arguments

compendium	A string - the selected compendium
samplesetNames	A character vector (sampleset names)
normalization	A string - either 'limma' (default),'tpm' or legacy as normalization
rank	A string ('magnitude' as default) - use get_ranking
top_n	A numeric - an integer for selecting the top ranked samplesets
sorted	A logical (FALSE as default) - it returns a sorted index for both bf and ss
useIds	A logical (FALSE as default) - It allows using samplesetIds

Value

A SummarizedExperiment object

Examples

if (FALSE) {
my_ids=c("U2FtcGxlU2V0VHlwZTo2NDE5","U2FtcGxlU2V0VHlwZToyMTg2OA==")
mod_ss <- create_module_ss(samplesetNames = my_ids,
normalization = "limma", top_n = 15, useIds = TRUE)
}