search

ramiromagno / gwasrapidd

gwasrapidd: an R package to query, download and wrangle GWAS Catalog data
https://rmagno.eu/gwasrapidd/
Other
88 stars 14 forks source link

to get a vairants list from GWAS catalog #48

Open GGboy-Zzz opened 3 weeks ago

GGboy-Zzz commented 3 weeks ago

Thanks you for this greate tool to access GWAS catalog datasets. I want to download the top associations SNPs from GWAS catalog, and convert it to a SNP variant list like bim file,

image yet the 'get_associations' output didnt have the SNP reference allele. Can you give me some help or suggestions to extract it from GWAS catalog? I will be deeply grateful.

ramiromagno commented 3 weeks ago

Hi @GGboy-Zzz,

I am happy to help.

Can you share some sample code of what you are trying to achieve? Namely, the early steps (querying criteria) for retrieving variants?

GGboy-Zzz commented 3 weeks ago

Thank for your quickly response. I'm retrieved variants from a list of studys on relative traits, code as follows, studies <- get_studies(efo_trait = 'melanoma') variants=get_variants(study_id='GCST000198') associations <- get_associations(study_id='GCST000198')

ramiromagno commented 5 days ago

Hi @GGboy-Zzz : I'm afraid the reference allele is not directly provided bythe GWAS Catalog.