The associations number obtained by "gwasrapidd" differs extremly from obtained in GWAS Catalog

[shenlan17]

Hi, Using the code as follows, only 182 associations obtained my_associations <- get_associations(efo_id = "EFO_0005140") but in the GWAS Catalog web. it shows more than 7000 associations

[ramiromagno]

Hi @shenlan17,

The difference stems from the fact that the GWAS Catalog Web interface automatically presents associations directly related to EFO_0005140 trait and its child traits.

If you uncheck the box "include child trait data", then the number of associations is also 182 associations (as with gwasrapidd).

[ramiromagno]

If you run get_associations() with EFO_0005140 and its child terms you get actually more variants: 8087.

library(gwasrapidd)

all_traits <- get_traits()
child_traits <- gwasrapidd::get_child_efo("EFO_0005140")$EFO_0005140
child_traits_in_gwas_cat <- all_traits[child_traits]

my_associations <- get_associations(efo_id = c("EFO_0005140", child_traits_in_gwas_cat@traits$efo_id))

n(my_associations)
#> [1] 8087

my_associations
#> An object of class "associations"
#> Slot "associations":
#> # A tibble: 8,087 × 18
#>    association_id pvalue pvalue_description pvalue_mantissa pvalue_exponent
#>    <chr>           <dbl> <chr>                        <int>           <int>
#>  1 36071897       1e- 11 <NA>                             1             -11
#>  2 36071902       1e-  7 <NA>                             1              -7
#>  3 36071907       3e- 18 <NA>                             3             -18
#>  4 36071911       2e-103 <NA>                             2            -103
#>  5 36071916       4e-  8 <NA>                             4              -8
#>  6 36071920       3e-  9 <NA>                             3              -9
#>  7 36071924       1e- 13 <NA>                             1             -13
#>  8 36071929       3e-  8 <NA>                             3              -8
#>  9 36071934       2e-  9 <NA>                             2              -9
#> 10 36071938       5e- 14 <NA>                             5             -14
#> # ℹ 8,077 more rows
#> # ℹ 13 more variables: multiple_snp_haplotype <lgl>, snp_interaction <lgl>,
#> #   snp_type <chr>, risk_frequency <dbl>, standard_error <dbl>, range <chr>,
#> #   or_per_copy_number <dbl>, beta_number <dbl>, beta_unit <chr>,
#> #   beta_direction <chr>, beta_description <chr>, last_mapping_date <dttm>,
#> #   last_update_date <dttm>
#> 
#> Slot "loci":
#> # A tibble: 8,089 × 4
#>    association_id locus_id haplotype_snp_count description   
#>    <chr>             <int>               <int> <chr>         
#>  1 36071897              1                  NA Single variant
#>  2 36071902              1                  NA Single variant
#>  3 36071907              1                  NA Single variant
#>  4 36071911              1                  NA Single variant
#>  5 36071916              1                  NA Single variant
#>  6 36071920              1                  NA Single variant
#>  7 36071924              1                  NA Single variant
#>  8 36071929              1                  NA Single variant
#>  9 36071934              1                  NA Single variant
#> 10 36071938              1                  NA Single variant
#> # ℹ 8,079 more rows
#> 
#> Slot "risk_alleles":
#> # A tibble: 8,121 × 7
#>    association_id locus_id variant_id risk_allele risk_frequency genome_wide
#>    <chr>             <int> <chr>      <chr>                <dbl> <lgl>      
#>  1 36071897              1 rs10797431 <NA>                    NA FALSE      
#>  2 36071902              1 rs72920202 <NA>                    NA FALSE      
#>  3 36071907              1 rs10494079 <NA>                    NA FALSE      
#>  4 36071911              1 rs2476601  <NA>                    NA FALSE      
#>  5 36071916              1 rs1800601  <NA>                    NA FALSE      
#>  6 36071920              1 rs11675342 <NA>                    NA FALSE      
#>  7 36071924              1 rs1534430  <NA>                    NA FALSE      
#>  8 36071929              1 rs67927699 <NA>                    NA FALSE      
#>  9 36071934              1 rs5865     <NA>                    NA FALSE      
#> 10 36071938              1 rs2075302  <NA>                    NA FALSE      
#> # ℹ 8,111 more rows
#> # ℹ 1 more variable: limited_list <lgl>
#> 
#> Slot "genes":
#> # A tibble: 8,563 × 3
#>    association_id locus_id gene_name
#>    <chr>             <int> <chr>    
#>  1 63818111              1 <NA>     
#>  2 55992578              1 MMEL1    
#>  3 55992585              1 PADI4    
#>  4 55992592              1 PTPN22   
#>  5 55992599              1 PTPN22   
#>  6 55992606              1 FASLG    
#>  7 55992613              1 AFF3     
#>  8 55992620              1 ITGA4    
#>  9 55992627              1 NAB1     
#> 10 55992634              1 STAT4    
#> # ℹ 8,553 more rows
#> 
#> Slot "ensembl_ids":
#> # A tibble: 10,815 × 4
#>    association_id locus_id gene_name ensembl_id     
#>    <chr>             <int> <chr>     <chr>          
#>  1 63818111              1 <NA>      <NA>           
#>  2 55992578              1 MMEL1     ENSG00000142606
#>  3 55992578              1 MMEL1     ENSG00000277131
#>  4 55992585              1 PADI4     ENSG00000159339
#>  5 55992585              1 PADI4     ENSG00000280908
#>  6 55992592              1 PTPN22    ENSG00000134242
#>  7 55992599              1 PTPN22    ENSG00000134242
#>  8 55992606              1 FASLG     ENSG00000117560
#>  9 55992613              1 AFF3      ENSG00000144218
#> 10 55992620              1 ITGA4     ENSG00000115232
#> # ℹ 10,805 more rows
#> 
#> Slot "entrez_ids":
#> # A tibble: 8,563 × 4
#>    association_id locus_id gene_name entrez_id
#>    <chr>             <int> <chr>     <chr>    
#>  1 63818111              1 <NA>      <NA>     
#>  2 55992578              1 MMEL1     79258    
#>  3 55992585              1 PADI4     23569    
#>  4 55992592              1 PTPN22    26191    
#>  5 55992599              1 PTPN22    26191    
#>  6 55992606              1 FASLG     356      
#>  7 55992613              1 AFF3      3899     
#>  8 55992620              1 ITGA4     3676     
#>  9 55992627              1 NAB1      4664     
#> 10 55992634              1 STAT4     6775     
#> # ℹ 8,553 more rows

^{Created on 2023-10-18 with reprex v2.0.2}

[ramiromagno]

Hi @shenlan17:

Did my replies address your question?

[shenlan17]

@ramiromagno yes, Thank you very much for your help!