find_associated_TFs: Given a list of genes, find which TFs they are associated...

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 TF activity data (by group, not by cell...optional) and a dataframe of cohen's D scores (if the comparison is 2 groups...optional). If only the gene vector is supplied, the function will return all TFs for which a given gene is part of the regulon for the entire dorothea collection of TFs.

Usage

find_associated_TFs(
  gene_vector,
  tf_data_bygroup = NULL,
  effect_size_data = NULL,
  custom_regulons = NULL
)

Arguments

gene_vector	vector of genes
tf_data_bygroup	TF 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_regulons	searches custom TF regulons for genes in gene vector, default is FALSE.

Examples

find_associated_TFs(gene_vector, tf_data_bygroup, effect_size_data, custom_regulons=custom_regulons)

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