calcSignatureScores: calculate signature scores

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

calculate signature scores

Description

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

Usage

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 June 14, 2024, 5:27 p.m.