README_analyses.md

Analyze Data with

Get the same analysis results from the command line as from Reactome's Analyse Data Tool GUI.

Table of Contents

• Output files
• Command-line Examples
• Command-line and Reactome GUI compared

Output Files

The pathway enrichment results are written into these files:

Reactome Name	ReactomePy Name
result.csv	pathway_enrichment.csv
result.pdf	pathway_enrichment.pdf
mapping.csv	ids_mapping.csv
not_found.csv	ids_notfound.csv

Command-line Examples

$ src/bin/pwy_enrichment_reactome.py data/enrich/studyids/1q21o3.txt

Command-line and Reactome GUI return the same results

1. Reactome Pathway Analysis
2. Load Study IDs
3. Write results to files

1) Reactome Pathway Analysis

Click on Analyze Data on Reactome's homepage to begin a pathway enrichment analysis.

2) Load Study IDs

Load the study ID file from the command line or in Reactome's Analyse Data Tool GUI.

3) Write results to files

Reactome Button	Reactome Name	ReactomePy Name
Result	result.csv	pathway_enrichment.csv
Report (PDF)	result.pdf	pathway_enrichment.pdf
Mapping	mapping.csv	ids_mapping.csv
Not found	not_found.csv	ids_notfound.csv

3a) Result and Mapping files

3b) Not found file

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