Normalize - normalize summed gene counts across samples. This is a wrapper around edgeR functions `calcNormFactors` and `filterByExpr`.

Normalize - normalize summed gene counts across samples. This is a wrapper around edgeR functions `calcNormFactors` and `filterByExpr`.

Usage

Normalize(
  pseudobulk.list,
  design,
  group = NULL,
  normalization.method = "RLE",
  minimum.gene.count = 1
)

Arguments

pseudobulk.list

object created with PseudobulkList only use this function if argument to PseudobulkList avg_or_sum was 'sum' computes normalization for pseudobulk libraries

design

see edgeR `filterByExpr` function. This is the design matrix created using model.matrix and e.g. the metadata created AggregateCellMetadata.

normalization.method

see edgeR function calcNormFactors, this is the argument to `method`

minimum.gene.count

see edgeR function `filterbyExpr` thie is the argument to `min.count`

Value

a list of dgeList objects indexed by celltype

Examples