calcModuleScores: Calculate module scores (signature scores but on the modules)

Description Usage Arguments Value

View source: R/methods-Module.R

Description

For each module-cell pair, compute a score that captures the level of correspondence between the cell and the module.

Usage

1
calcModuleScores(object, mod_norm_method = NULL, mod_gene_importance = TRUE)

Arguments

object

the VISION object

mod_norm_method

Method to apply to normalize the expression matrix before calculating signature scores. Valid options are: "znorm_columns" (default), "none", "znorm_rows", "znorm_rows_then_columns", or "rank_norm_columns"

mod_gene_importance

whether or not to rank each gene's contribution to the overall signature score. Default = TRUE. This is used for inspecting genes in a signature in the output report

Value

the VISION object, with the @ModScores and @ModGeneImportance slots populated


YosefLab/VISION documentation built on Sept. 14, 2021, 5:27 p.m.