scMetaTraj (version 0.1.1)

scMetaTraj_score: Calculate metabolic pathway scores for single cells

Description

scMetaTraj_score() maps gene-level expression to pathway-level metabolic activity scores. The resulting matrix defines the metabolic feature space used by all downstream scMetaTraj modules.

IMPORTANT:

• Scores represent relative metabolic states, NOT metabolic flux.

• Designed to be robust to dropout in scRNA-seq data.

Usage

scMetaTraj_score(
  x,
  gene_sets,
  assay = "RNA",
  slot = "data",
  method = c("mean", "zscore"),
  min_genes = 3,
  scale = TRUE
)

Value

A numeric matrix: cells x pathways.

Arguments

x

A Seurat object or a gene x cell expression matrix.

gene_sets

A named list: pathway -> character vector of genes.

assay

Character. Seurat assay to use. Default "RNA".

slot

Character. Expression slot. Default "data".

method

Character. Scoring method: "mean" or "zscore".

min_genes

Integer. Minimal number of detected genes per pathway.

scale

Logical. Whether to z-score pathway scores across cells.