handle_pyscenic_results: Uses reticulate package to handle and process the results...

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

handle pySCENIC results

Usage

handle_pyscenic_results(
  dir,
  output_loom_path,
  anndata_path,
  comparison_feature = "cell_type",
  regulon_path
)

Arguments

dir	directory path to output pySCENIC results
output_loom_path	path to output loom file
anndata_path	path to initial anndata object
comparison_feature	which obs feature from the anndata should we look at? for RSS.
regulon_path	path to the regulon output from CisTarget
regulon_output_fname	file name for writing processed regulons (.csv)
auc_mtx_fname	filename for writing AUC matrix (.csv)
cellannot_fname	filename for writing cellAnnot matrix (.csv)
RSS_fname	filename for writing regulon specificity scores matrix (.csv)

Examples

handle_pyscenic_results(dir, output_loom_path, anndata_path, comparison_feature="cell_type", regulon_path)

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