makeDGEList: Make a DGEList object.

In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description

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

Usage

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

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.