find_associated_pathways: Given a list of genes, find which pathways they are...

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

This function takes a vector of genes and pathway activity data (by group, not by cell...optional) and a data frame of cohen's D scores (if the comparison is 2 groups...optional). If only the gene vector is supplied, the function will return all pathways for which a given gene is part of the pathway's gene set.

Usage

find_associated_pathways(
  gene_vector,
  pathway_data_bygroup = NULL,
  effect_size_data = NULL,
  custom_pathways = NULL,
  progeny_pathways = TRUE,
  num_genes = 500,
  organism = "Human"
)

Arguments

gene_vector	vector of genes
pathway_data_bygroup	pathway data summarized by comparison group
effect_size_data	dataframe of cohen's D scores for a given comparison (optional, only if comparison is 2 groups)
custom_pathways	searches custom pathways for genes in gene vector, default is FALSE.

Examples

find_associated_pathways(gene_vector, pathway_data_bygroup, effect_size_data, custom_pathways=custom_pathways, progeny_pathways=FALSE)

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