Calculate Miko module scores for feature expression programs

Feature expression programs are scored by first computing standardized module scores with `AddSModuleScore` and then scaling the scores by the null distributions calculated using `nullScore`. The resulting scores are robust to gene set size and can be further used to compute whether feature expression program is significantly up-regulated in single-cell population.

mikoScore(
  object,
  geneset,
  nullscore,
  do.center = F,
  do.scale = T,
  assay = DefaultAssay(object),
  nworkers = 1,
  nbin = 24,
  verbose = T
)

Arguments

object

Seurat Object

geneset

A list of vectors of features for expression programs; each entry should be a vector of feature names

nullscore

`nullScore` output for provided `object`. Must run `nullScore` prior to running `mikoScore`.

do.center

center scores using null model predictions. Default is FALSE.

do.scale

scale scores by null model variance predictions. Default is TRUE.

assay

Name of assay to use.

nworkers

Number of workers for parallel implementation. Default is 1.

nbin

Number of bins of aggregate expression levels for all analyzed features. See `AddModuleScore` for details.

verbose

Print progress. Default is TRUE.

Value

list of results.

See also

AddSModuleScore for standardized module scoring, nullScore for calculating null score distributions sigScore for derivation of p values for miko scores.

Author

Nicholas Mikolajewicz