AddSModuleScore: Calculate standardized module scores for feature expression...

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Calculate standardized module scores for feature expression programs in single cells.

Description

Calculates the standardized expression level of each program on single-cell level, by subtracting by aggregated expression of control feature sets (like in 'AddModuleScore') and then scaling the difference by the pooled variance of the gene set of interest and control features. Like 'AddModuleScore', all analyzed features are binned based on averaged expression and control features are randomly selected from each bin.

Usage

AddSModuleScore(
  object,
  features,
  pool = NULL,
  nbin = NULL,
  ctrl = 100,
  nworkers = 1,
  scale = T,
  k = FALSE,
  assay = NULL,
  name = "Cluster",
  seed = 1,
  search = FALSE,
  ...
)

Arguments

object	Seurat Object
features	A list of vectors of features for expression programs; each entry should be a vector of feature names
pool	List of features to check expression levels against, 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
nworkers	Number of workers for parallel implementation. Default is 1.
scale	scale score by pooled variance. Default is T.
k	Use feature clusters returned from DoKMeans
assay	Name of assay to use
name	Name for the expression programs; will append a number to the end for each entry in features (eg. if 'features' has three programs, the results will be stored as name1, name2, name3, respectively)
seed	Set a random seed. If NULL, seed is not set.
search	Search for symbol synonyms for features in features that don't match features in object? Searches the HGNC's gene names database; see UpdateSymbolList for more details
...	Extra parameters passed to UpdateSymbolList

Value

Returns seurat object with standardized module scores added to object meta data; each module is stored as name# for each module program present in 'features'

Author(s)

Nicholas Mikolajewicz

See Also

AddModuleScore for original module scoring function implemented in 'Seurat'.

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.