create a module based on provided biological features
create_module_bf( compendium = "vespucci", biofeaturesNames = NULL, normalization = "limma", rank = "magnitude", top_n = 50, sorted = FALSE, useIds = FALSE )
compendium | A string - the selected compendium |
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biofeaturesNames | A character vector (gene_names) |
normalization | A string - either 'limma' (default),'tpm' or legacy as normalization |
rank | A string ('magnitude' as default) |
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 biofeatureIds |
A SummarizedExperiment object
if (FALSE) { my_bf <- c("VIT_00s0246g00220","VIT_00s0332g00060","VIT_00s0332g00110") tmp <- get_biofeature_id(id_In = my_bf, useIds = F)$id my_mod <- create_module_bf(biofeaturesNames= tmp, normalization = "limma", top_n = 15, useIds = T) }