Description Usage Arguments Value Examples
create a module based on provided sample sets
1 2 3 4 5 6 7 8 9 | create_module_ss(
compendium = "vespucci",
samplesetNames = NULL,
normalization = "limma",
rank = "uncentered_correlation",
top_n = 50,
sorted = FALSE,
useIds = FALSE
)
|
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 |
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 |
A SummarizedExperiment object
1 2 3 4 5 6 | ## Not run:
my_ids=c("U2FtcGxlU2V0VHlwZTo2NDE5","U2FtcGxlU2V0VHlwZToyMTg2OA==")
mod_ss <- create_module_ss(samplesetNames = my_ids,
normalization = "limma", top_n = 15, useIds = TRUE)
## End(Not run)
|
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