List of Variants to GWAS associations

[lizlitkowski]

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]

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]

Hi Ramiro,

Thank you so much.

This is exactly what I am looking for!

I ran it for my 331 SNPs and it only took about 10-15 minutes.

I will be keeping this in my bag of tricks.

Thank you!!!!

Best, Liz

On Tue, May 16, 2023 at 8:05 PM Ramiro Magno @.***> wrote:

[External Email - Use Caution]

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 variantsmy_variants <- c("rs7329174", "rs3798440")my_variants <- setNames(my_variants, nm = my_variants)

lst <- purrr::map(my_variants, ~ get_associations(variant_id = .@.[, "association_id"])var_to_assoc <- purrr::list_rbind(lst, names_to = "variant_id") my_associations <- var_to_assoc$association_idmy_associations <- setNames(my_associations, nm = my_associations)lst2 <- purrr::map(my_associations, ~ get_traits(association_id = .@.[, 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 #> #> 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

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[ramiromagno]

You're welcome!