Help Needed: Importing and Analyzing GWAS Data from GWAS Catalog in R

Question

[城玮]

Hello everyone,

I hope this message finds you well. I am currently working on a project that involves using data from the GWAS Catalog. I have successfully obtained the GWAS data, but I am facing challenges with importing and analyzing this data in R.

I used following code to obtain the data from GWAS catalog:

vagina_study <- get_studies(efo_trait = 'vaginal microbiome measurement')
vagina_association <- get_associations(study_id = vagina_study@studies$study_id)

The vagina_association has following parts:

associations:

  association_id    pvalue pvalue_description
  <chr>              <dbl> <chr>
1 62275861       0.000005  NA
2 62275867       0.000007  NA
3 62275877       0.0000007 NA
4 62275882       0.000002  NA
5 62275887       0.000004  NA

loci:

  association_id locus_id haplotype_snp_count
  <chr>             <int>               <int>
1 62275861              1                  NA
2 62275867              1                  NA
3 62275877              1                  NA

risk_alleles:

  association_id locus_id variant_id risk_allele
  <chr>             <int> <chr>      <chr>
1 62275861              1 rs1229660  C
2 62275867              1 rs10414170 C
3 62275877              1 rs527430   A

genes:

  association_id locus_id gene_name
  <chr>             <int> <chr>
1 62275861              1 SNX10
2 62275861              1 LOC441204
3 62275867              1 ZIM2-AS1

ensembl_ids:

  association_id locus_id gene_name ensembl_id
  <chr>             <int> <chr>     <chr>
1 62275861              1 SNX10     ENSG00000086300
2 62275861              1 LOC441204 NA
3 62275867              1 ZIM2-AS1  ENSG00000269793

entrez_ids:

  association_id locus_id gene_name entrez_id
  <chr>             <int> <chr>     <chr>
1 62275861              1 SNX10     29887
2 62275861              1 LOC441204 NA
3 62275867              1 ZIM2-AS1  101929059

I would like to import the aforementioned data into an R package that can perform subsequent Mendelian randomization analysis, such as the TwoSampleMR package, but I don't know the specific method.

Could anyone provide a step-by-step guide or any resources on how to import GWAS data from the GWAS Catalog into R and perform subsequent analyses, specifically MR analysis? Any advice on packages, functions, or best practices would be greatly appreciated.

Thank you in advance for your help!

Best regards,
Zhang Chengwei