Normalize: Normalize - normalize summed gene counts across samples. This...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

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

Description

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

#' #'\dontrun{
}

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.