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# This cell contains default parameters values for execution by `papermill`.
filename = '../sample_data/postgap.20180817.asthma.txt.gz'

POSTGAP Report

This notebook was automatically generated as a summary of POSTGAP output.

Setup

Note that for command line usage (python reporter.py <filename>) the following will work just fine. However, to edit the template, temporarily change the following to import helpers.



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from reports import helpers



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helpers.calc_run_str()



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# pg = pd.read_csv(filename, sep='\t', na_values=['None'])
pg = helpers.load_file(filename)

Headline

Q: How many rows and columns?



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print(pg.shape)

Q: How many unique target-disease associations?



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helpers.calc_g2d_pair_counts(pg)

Q: What is the distribution of unique diseases per gene? And vice versa?



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helpers.calc_pairwise_degree_dist(pg, 'gene_id', 'disease_efo_id', 'Gene', 'Disease')

Identifiers

Q: How many unique values appear for each identifier?



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helpers.calc_id_field_counts(pg)

Q: What is the maximum number of rows for a given fixed identifier?



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helpers.calc_id_field_max_rows(pg)

Identifier pairs

Q: How many unique identifier pairs appear?



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helpers.calc_id_field_pair_counts(pg)

Gene-LD SNP associations

Q: What is the distribution of each association subscore (VEP, GTEx, etc.)?



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helpers.calc_g2v_field_hists(pg)

Q: What is the distribution of unique LD SNPs per gene? And vice versa?



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helpers.calc_pairwise_degree_dist(pg, 'gene_id', 'ld_snp_rsID', 'Gene', 'LD SNP')

Q: What is the overlap between presence of association subscores?



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helpers.calc_g2v_field_overlap(pg)

Q: What is the joint distribution between association subscore pairs (ie. how correlated are they)?



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helpers.calc_g2v_field_cross_dists(pg)

LD SNP-GWAS SNP associations

Q: What is the distribution of r2?



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helpers.calc_dist_r2(pg)

Q: What is the distribution of unique GWAS SNPs per LD SNP? And vice versa?



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helpers.calc_pairwise_degree_dist(pg, 'ld_snp_rsID', 'gwas_snp', 'LD SNP', 'GWAS SNP')

GWAS SNP-Disease associations

Q: What are the distributions of (gwas_pvalue, gwas_beta, gwas_odds_ratio)?



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helpers.calc_v2d_field_hists(pg)

Q: What is the distribution of unique diseases per GWAS SNP? And vice versa?



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helpers.calc_pairwise_degree_dist(pg, 'gwas_snp', 'disease_efo_id', 'GWAS SNP', 'Disease')