ssc.moduleScore: Add module scores for gene expression programs in single...

In Japrin/sscVis: simpler single cell RNAseq data Visualization

Add module scores for gene expression programs in single cells. Mofidy from Seurat::AddModuleScore

Description

Calculate the average expression levels of each program (cluster) on single cell level, subtracted by the aggregated expression of control feature sets. All analyzed features are binned based on averaged expression, and the control features are randomly selected from each bin.

Usage

ssc.moduleScore(
  obj,
  features,
  pool = NULL,
  nbin = 24,
  ctrl = 100,
  assay.name = "exprs",
  adjB = NULL,
  do.scale = T,
  seed = 1
)

Arguments

obj	object of SingleCellExperiment
features	Feature expression programs in named list
pool	List of features to check expression levels agains, defaults to rownames(x = object)
nbin	Number of bins of aggregate expression levels for all analyzed features
ctrl	Number of control features selected from the same bin per analyzed feature
assay.name	Name of assay to use
adjB	character; batch column of the colData(obj). (default: NULL)
do.scale	logical; scale the data (default: TRUE)
seed	Set a random seed

Value

Returns a SingleCellExperiment object with module scores added to object meta data

References

Tirosh et al, Science (2016); Seurat's source code

Japrin/sscVis documentation built on March 5, 2025, 10:23 a.m.