select DEGs from multiple comparisons

select_sig(tfit, feature_selection = c("auto", "rankproduct", "none"), ...)

Arguments

tfit: processed tfit by limma::treat() or processed data returned by process_data()
feature_selection: one of "auto" (default), "rankproduct" or "none", choose if to use rank product or not to select DEGs from multiple comparisons of DE analysis, 'auto' uses 'rankproduct' but change to 'none' if final genes < 5 for both UP and DOWN
...: params for DEGs_RP() or DEGs_Group()

Value

GeneSetCollection contains UP and DOWN gene sets

Examples

data("im_data_6")
proc_data <- process_data(
  im_data_6,
  group_col = "celltype:ch1",
  target_group = "NK"
)
#>        NK-Neutrophils NK-Monocytes NK-B.cells NK-CD4 NK-CD8
#> Down             4009         3944       3146   2694   2153
#> NotSig           1476         2678       4405   4985   6183
#> Up               4926         3789       2860   2732   2075
select_sig(proc_data$tfit)
#> GeneSetCollection
#>   names: UP, DOWN (2 total)
#>   unique identifiers: ENSG00000149294, ENSG00000173068, ..., ENSG00000162591 (96 total)
#>   types in collection:
#>     geneIdType: NullIdentifier (1 total)
#>     collectionType: NullCollection (1 total)