ramiromagno/gwasrapidd

List of Variants to GWAS associations

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lizlitkowski commented

Hi -- Is there a function where I can specify a list of variants and get back a list of traits those variants have been associated with in GWAS studies?
Thanks.
Liz

ramiromagno commented

Hi Liz,

One variant can be implicated in many associations and each association associated with a single trait. Because the mapping from variants to associations is one to many, in {gwasrapidd} we have to take this path of mapping from variants to associations to traits explicitly... In the future I might implement this in a more straightforward way for the user (apologies for that!).

For the moment the following code should do the trick:

library(gwasrapidd)
library(tidyverse)

# Adapt `my_variants` to be a vector of your variants
my_variants <- c("rs7329174", "rs3798440")
my_variants <- setNames(my_variants, nm = my_variants)

lst <- purrr::map(my_variants, ~ get_associations(variant_id = .x)@associations[, "association_id"])
var_to_assoc <- purrr::list_rbind(lst, names_to = "variant_id")

my_associations <- var_to_assoc$association_id
my_associations <- setNames(my_associations, nm = my_associations)
lst2 <- purrr::map(my_associations, ~ get_traits(association_id = .x)@traits[, c("efo_id", "trait")])
assoc_to_trait <- purrr::list_rbind(lst2, names_to = "association_id")

left_join(var_to_assoc, assoc_to_trait, by = "association_id")
#> # A tibble: 7 × 4
#>   variant_id association_id efo_id        trait                       
#>   <chr>      <chr>          <chr>         <chr>                       
#> 1 rs7329174  16617          MONDO_0007915 systemic lupus erythematosus
#> 2 rs7329174  26451          EFO_0000384   crohn's disease             
#> 3 rs7329174  26394          MONDO_0007915 systemic lupus erythematosus
#> 4 rs7329174  92481688       MONDO_0007915 systemic lupus erythematosus
#> 5 rs7329174  17433639       MONDO_0007915 systemic lupus erythematosus
#> 6 rs7329174  103267749      EFO_0004339   body height                 
#> 7 rs3798440  24299710       EFO_0000537   hypertension
lizlitkowski commented
ramiromagno commented

You're welcome!