Null distribution for standardized module scores.

Downsample number of cells in Seurat object by specified factor

nullScore(
  object,
  assay = DefaultAssay(object),
  n.replicate = 25,
  min.gs.size = 2,
  max.gs.size = 100,
  step.size = 2,
  nworkers = 1,
  subsample.n = NULL,
  nbin = 24,
  verbose = T
)

Arguments

object

Seurat Object

assay

Name of assay to use

n.replicate

Number of replicates

min.gs.size

minimum gene set size

max.gs.size

maximum gene set size

step.size

step size; increment of sequence between `min.gs.size` and `max.gs.size`.

nworkers

number of workers used for parallel implementation. Default is 1.

subsample.n

Numeric [1,ncol(object)]. Number of cells to subsample. If specified, overides subsample.factor.

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 that are used as input into `mikoScore`.

See also

AddSModuleScore for standardized module scoring, mikoScore for miko scoring, sigScore for derivation of p values for miko scores.

Author

Nicholas Mikolajewicz