Class: CredibleSetLZ

LocusZoom_Adapters~CredibleSetLZ()

(extension) Custom data adapter that calculates the 95% credible set based on provided association data. This source must be requested as the second step in a chain, after a previous step that returns fields required for the calculation. (usually, it follows a request for GWAS summary statistics)

Constructor

new CredibleSetLZ()

Parameters:
Name Type Attributes Default Description
config.params.threshold Number <optional>
 0.95

The credible set threshold (eg 95%). Will continue selecting SNPs until the posterior probabilities add up to at least this fraction of the total.
config.params.significance_threshold Number <optional>
 7.301

Do not perform a credible set calculation for this region unless AT LEAST ONE SNP (as -log10p) exceeds the line of GWAS signficance. Otherwise we are declaring a credible set when there is no evidence of anything being significant at all. If one snp is significant, it will create a credible set for the entire region; the resulting set may include things below the line of significance.
Source:
See: