Description Usage Arguments Value Examples
create a module providing both biological features and sample sets
1 2 3 4 5 6 7 8 | create_module(
compendium = "vespucci",
normalization = "limma",
biofeaturesNames = NULL,
samplesetNames = NULL,
sorted = FALSE,
useIds = FALSE
)
|
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 |
A SummarizedExperiment object
1 2 3 4 5 6 7 8 9 10 11 12 13 | ## Not run:
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"))
## End(Not run)
|
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