SEMtree/README.md

In fernandoPalluzzi/SEMgraph: Network Analysis and Causal Inference Through Structural Equation Modeling

SEMtree: tree-based structure learning methods with Structural Equation Models

by Mario Grassi and Barbara Tarantino

R code corresponding author: Barbara Tarantino ([e-mail])

 

This section contains R code and data for the SEMtree project reproducibility.

The folder structure can be summarised as follows:

./code/:

tree_sim.R
An R script to run Data simulations

tree_bench.R
An R script to run True data analysis

tree_comparison.R
An R script to run Method comparison

Help.R
An R script with functions to import for running the analysis

./data/:

C0206750_disease_gda_summaryGSE172114_rsem_gene_count_matrix_TMM_69samples.csv
GA_result.Rdata
Gores.txt
GSE172114_rsem_gene_count_matrix_TMM_69samples.csv
GSE172114_series_matrix.txt.gz
ijmsv19p0402s2.xlsx

./graph/:

BioNet
COSINE
KEGGCovid19.graph
pathfinder
ST
STcfa
STcov
Stone
STr2z
STr2zN
STsem
tree_base
WalktrapGM
WalktrapGMl

Notes

1. Set SEMtree_code_data as the current working directory.
2. To reduce computing time for data simulations, reduce the number of iterations through the argument “seed_vec”.

Data source

The original data used in this research can be downloaded at GSE172114.

References

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fernandoPalluzzi/SEMgraph documentation built on Feb. 20, 2025, 4:27 p.m.