WeightedCellModuleScore: WeightedCellModuleScore - calculate the average or weighted...

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

WeightedCellModuleScore - calculate the average or weighted aveage +/- scaling return dataframe of cells by average module score

Description

WeightedCellModuleScore - calculate the average or weighted aveage +/- scaling return dataframe of cells by average module score

Usage

WeightedCellModuleScore(
  gene_matrix = NULL,
  module_list,
  threshold = 0,
  cellwise_scaling = FALSE,
  return_weighted = FALSE
)

Arguments

gene_matrix	- normalized genes (rows) by cells (columns)
module_list	- names list of gene modules - each element a vector of gene names.
threshold	- at least this fraction of genes in the signature must be < 0 across all cells or else a score is not calculated
cellwise_scaling	- T/F scale across cells ?
return_weighted	- T/F weight the averae by multiplying by gene representation?

Value

dataframe of cells barcodes (rownames) by gene module scores (columns)

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