create a module providing both biological features and sample sets

create a module providing both biological features and sample sets

create_module(
  compendium = "vespucci",
  normalization = "limma",
  biofeaturesNames = NULL,
  samplesetNames = NULL,
  sorted = FALSE,
  useIds = FALSE
)

Arguments

compendium	A string - the selected compendium
normalization	A string - either 'limma' (default),'tpm' or legacy as normalization
biofeaturesNames	A character vector (gene_names)
samplesetNames	A character vector (sampleset names)
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

Value

A SummarizedExperiment object

Examples

if (FALSE) {
gene_names <- c("VIT_00s0246g00220","VIT_00s0332g00060","VIT_00s0332g00110",
"VIT_00s0332g00160","VIT_00s0396g00010","VIT_00s0505g00030",
"VIT_00s0505g00060","VIT_00s0873g00020","VIT_00s0904g00010")
mod_bf <- create_module(biofeaturesNames = gene_names)
my_bf <- get_biofeature_id(id_In = gene_names, useIds = FALSE)
ss=c("GSE75498_OS_T0-13-vs-GSE75498_C_T0-21","harvest_4","harvest_5")
my_ss <- get_sampleset_id(id_In = ss, normalization = "limma", useIds = FALSE)
my_mod <- create_module(biofeaturesNames = my_bf$id, samplesetNames = my_ss$id,
normalization = "limma", useIds = TRUE)
pheatmap::pheatmap(na.omit(Biobase::exprs(my_mod)), col = RColorBrewer::brewer.pal(11,name="RdBu"))
}