NormalizePseudobulk: NormalizePseudobulk

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

NormalizePseudobulk

Description

NormalizePseudobulk

Usage

NormalizePseudobulk(
  pseudobulklist,
  normalization.method = "RLE",
  design_matrix,
  minimum.gene.count = 1
)

Arguments

pseudobulklist	object created with PseudobulkList only use this function if argument to PseudobulkList avg_or_sum was 'sum' computes normalization for pseudobulk libraries
normalization.method	see edgeR function calcNormFactors, this is the argument to 'method'
design_matrix	the sample level metadata created by AggregateCellMetadata which will be used to make the designamatrix.
minimum.gene.count	see edgeR function 'filterbyExpr' thie is the argument to 'min.count'

Value

a list of dgeList indexed by celltype

Examples

#' #'\dontrun{
}
# normalize the pseudobulk data made with MakePseudobulkList

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