AddModuleScore: Calculate module scores for gene expression programs in...

In mayer-lab/SeuratForMayer2018: Seurat : R Toolkit for Single Cell Genomics

Description

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

Usage

AddModuleScore(object, genes.list = NULL, genes.pool = NULL, n.bin = 25,
  seed.use = 1, ctrl.size = 100, use.k = FALSE, enrich.name = "Cluster")

Arguments

object	Seurat object
genes.list	Gene expression programs in list
genes.pool	List of genes to check expression levels agains, defaults to rownames(x = object@data)
n.bin	Number of bins of aggregate expression levels for all analyzed genes
seed.use	Random seed for sampling
ctrl.size	Number of control genes selected from the same bin per analyzed gene
use.k	Use gene clusters returned from DoKMeans()
enrich.name	Name for the expression programs

Value

Returns a Seurat object with module scores added to [e-mail]

References

Tirosh et al, Science (2016)

mayer-lab/SeuratForMayer2018 documentation built on May 25, 2019, 9:34 p.m.