Repository for code associated with the somatic instability analysis from the manuscript "Pathogenic Huntingtin Repeat Expansions in Patients with Frontotemporal Dementia and Amyotrophic Lateral Sclerosis"
Preprint: http://dx.doi.org/10.2139/ssrn.3652331
Input Files
- Sample key (tab-delimited .txt file) containing the following columns (no heading) for each region (separate file for each sample):
- File path for peak tables (.txt) direct output files from GeneMapper (4.0)
- Region name
- Modal peak height (manual verification based on observation of peak table and chromatogram)
- Modal peak size (manual verification based on observation of peak table and chromatogram)
- Peak tables (direct output files from GeneMapper)
- Heatmap input dataframe (tab-delimited .txt file) containing the following columns (no heading):
- Sample name that region corresponds to
- Region name
- Instability index for corresponding region
Somatic_Instability_Analysis.ipynb
Somatic instability analyses using input files listed above.