Make genome-wide significance thresholds configurable - Githubissues

statgen / pheweb

A tool to build a website to browse hundreds or thousands of GWAS.

MIT License

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Make genome-wide significance thresholds configurable #49

Closed pjvandehaar closed 3 years ago

pjvandehaar commented 7 years ago

5e-8 is used by:

[ ] other-phenos-for-gene
[ ] /random
[ ] Manhattan plot (just the line/tooltip)
- use window.model
[ ] LocusZoom plot (just the line)

1e-6 is used by:

[x] top_hits
[x] top_loci

(See https://github.com/statgen/pheweb/compare/master...phuwanat:master for reference.)

so,

[ ] Replace 5e-8 with conf.genome_wide_sig_threshold.
[x] Replace 1e-6 with conf.peak_pval_cutoff.

pjvandehaar commented 3 years ago

I don't want this.