Make final object for internal use by the app — make_final

This function takes an uploaded object and sanitizes it to make sure it is suitable for internal use along with other additions:

adds a 'dds_mapping' element that maps dds_list keys to res_list objects.
if there are multiple dds_list objects, it adds a 'all_dds' element combining all samples.

Usage

make_final_object(obj)

Arguments

obj: list object containing lists of DE analysis results, functional enrichment objects, pattern analysis objects & raw and normalized counts objects.

Value

final carnation object with additional pre-processing

Examples

if (FALSE) { # interactive()
library(DESeq2)

# make example DESeq dataset
dds <- makeExampleDESeqDataSet()

# run DE analysis
dds <- DESeq(dds)

# extract comparison of interest
res <- results(dds, contrast = c("condition", "A", "B"))

# perform VST normalization
rld <- varianceStabilizingTransformation(dds, blind = TRUE)

# build minimal object
obj <- list(
           res_list = list(
                          comp = list(
                              res = res,
                              dds = "main",
                              label = "A vs B"
                          )
                      ),
           dds_list = list(main = dds),
           rld_list = list(main = rld)
       )

# final object
final_obj <- make_final_object(obj)
}