calculate_PAS: calculation Pathway Activity Score

In ZhangBuDiu/PASBench: benchmarking study of seven (PAS) tools for scRNA-seq analysis

Description

parameters 'counts', 'gSets_path' and 'gSets' are consistent across all tools

Usage

calculate_PAS(
  counts,
  tool,
  species = "none",
  pathway = "none",
  gmt_file = "none",
  filter = F,
  normalize = "sctransform",
  n_cores = 3,
  rand_seed = 123
)

Arguments

counts	gene expresion matrix, rows are genes and cols are cells
tool	tool name
species	species; human or mouse
pathway	abbreviation for pathway database
gmt_file	pathways in GMT format
filter	whether filtering for genes expressed in less than 5 percent cells
normalize	normalization method

Details

other parameters see details of tools

Examples

counts = load_counts()
score = calculate_PAS(counts, 'AUCell', 'human','kegg')

ZhangBuDiu/PASBench documentation built on Sept. 26, 2021, 1:30 a.m.