I have came across a potential issue when using gwasrapidd to get associations with traits, for which multiple SNPs are reported (this is, the association is with an haplotype).
For example, when you run:
get_associations(study_id = "GCST000480"), we pull three associations as reported in the GWAS catalog, but when we inspect the risk_alleles slot, the risk allelic frequency (RAF) (or risk_frequency in gwasrapidd) for the individual SNPs isn't reported.
This means that the RAF that is displayed on the GWAS catalog web interface (which I assume corresponds to the haplotype RAF) is not displayed at all in the gwasrapidd interface.
Despite this small issue, I am loving your tool! Thank you so much!
I have came across a potential issue when using
gwasrapiddto get associations with traits, for which multiple SNPs are reported (this is, the association is with an haplotype).For example, when you run:
get_associations(study_id = "GCST000480"), we pull three associations as reported in the GWAS catalog, but when we inspect therisk_allelesslot, the risk allelic frequency (RAF) (orrisk_frequencyingwasrapidd) for the individual SNPs isn't reported.This means that the RAF that is displayed on the GWAS catalog web interface (which I assume corresponds to the haplotype RAF) is not displayed at all in the
gwasrapiddinterface.Despite this small issue, I am loving your tool! Thank you so much!