Make a DGEList object.

Make a DGEList object based on assay(object, "counts").

makeDGEList(
  x,
  group = NULL,
  rm_low_genes = TRUE,
  calc_norm = TRUE,
  min_count = 10
)

Arguments

x

A BbcSE object.
group

Name of a column from colData(). See ?edgeR::DGEList.
rm_low_genes

logical indicating whether low count genes should be removed. Implements edgeR::filterByExpr. Filters DGEList only.
calc_norm

logical indicating whether normalization factors should be calculated. Implements edgeR::calcNormFactors. Also turns on calculations of normalized counts and per-group normalized counts
min_count

numeric. Used only if rm_low_genes=TRUE. Sets min.count for edgeR::filterByExpr.

Value

A BbcSE object.

See also

filterByExpr