nullScore: Null distribution for standardized module scores.

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

Null distribution for standardized module scores.

Description

Downsample number of cells in Seurat object by specified factor

Usage

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'.

Author(s)

Nicholas Mikolajewicz

See Also

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

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