mikoScore: Calculate Miko module scores for feature expression programs

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

Calculate Miko module scores for feature expression programs

Description

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.

Usage

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.

Author(s)

Nicholas Mikolajewicz

See Also

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

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