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Return the DGEList

get_dge_list.Rd

Builds an edgeR DGEList from the filtered counts, library sizes and normalisation factors stored in the BulkDge() class. bixverse does not need edgeR itself, so this requires edgeR to be installed. Normalisation factors are one until normalise_bulk_dge() has run.

Usage

get_dge_list(object)

Arguments

object

BulkDge class.

Value

An edgeR DGEList, or NULL with a warning if qc_bulk_dge() has not been run.

Examples

# the edgeR DGEList built during QC
syn <- synthetic_bulk_cor_matrix()
meta <- data.table::data.table(
  sample_id = colnames(syn$counts),
  case_control = rep(c("case", "control"), each = 50)
)
object <- BulkDge(raw_counts = syn$counts, meta_data = meta)
object <- qc_bulk_dge(object, group_col = "case_control", .verbose = FALSE)
if (requireNamespace("edgeR", quietly = TRUE)) {
  dim(get_dge_list(object))
}
#> [1] 997  98