List of Variants to GWAS associations about gwasrapidd HOT 3 CLOSED

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 #> <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 — Reply to this email directly, view it on GitHub <#40 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHOH45GGKTWWZMX2N45UG4DXGQI5XANCNFSM6AAAAAAYEIOBMA> . You are receiving this because you authored the thread.Message ID: ***@***.***>