calcSignatureScores: calculate signature scores

Description Usage Arguments Value

View source: R/AnalysisFunctions.R

Description

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

Usage

1
calcSignatureScores(object, sig_norm_method = NULL, sig_gene_importance = TRUE)

Arguments

object

the VISION object

sig_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"

sig_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 @SigScores and @SigGeneImportance slots populated


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