custom_pathways_calc: Calculate pathway activity using a dataframe of custom...

In zcollest/scRegNetwrapper: Wrapper functions for single cell regulatory network analysis (DoRothEA, PROGENy, pySCENIC) as well as tools for downstream analysis and method comparisons.

Description

Uses the PROGENy framework to quantify pathway activity given a data frame of custom pathways and returns a Seurat object assay with the results.

Usage

custom_pathways_calc(
  seurat_obj,
  pathways,
  num_genes,
  organism = "Human",
  assay_name
)

Arguments

seurat_obj	seurat object
pathways	data frame of custom pathways (must be same format as PROGENy pathways)
num_genes	number of top genes to return for each pathway if full_model = FALSE.
organism	"Human" or "Mouse", defaults to "Human".
assay_name	string to name the resulting Seurat object assay

Examples

custom_pathways_calc(seurat_obj, pathways, 500, "Human", "custom_pathway_activity"))

zcollest/scRegNetwrapper documentation built on Dec. 23, 2021, 9:14 p.m.