Calculate Miko score significance

Miko scores are transformed to p values and corrected for multiple-comparisons using Benjamini Hochberg method.

sigScore(object, geneset, reduction = "umap")

Arguments

object

Seurat Object. Must contain miko scores (i.e., must run `mikoScore` prior to `sigScore`)

geneset

gene set list used for miko scoring (i.e., those provided as input into `mikoScore`).

reduction

Dimensionality reduction to add to cell-level statistics data.frame. Intended for downstream use (e.g., viewing miko scores in UMAP space).

Value

list of data frames containing cell- and cluster-level statistics. Also return plot comparing raw (unstandardized) module score with Miko scores.

See also

AddSModuleScore for standardized module scoring, mikoScore for miko scoring

Author

Nicholas Mikolajewicz