Closed james-cranley closed 1 year ago
Hi James,
Thanks for reporting this issue.
If you use the warnings = TRUE
and verbose = TRUE
, you should be able to spot the problematic SNP.
I can look more closely into your code but I will need a reproducible example. Could you share the contents of the EBI_codes.csv
file?
not sure if this is what you're trying to achieve... but here it goes:
library('gwasrapidd')
library('tidyverse')
efo_traits <- c('aortic valve disease', 'heart valve disease','coronary artery disease')
efos <- get_traits(efo_trait = efo_traits)
my_assoc <- get_associations(efo_id = efos@traits$efo_id)
my_assoc@risk_alleles
# A tibble: 2,788 × 7
association_id locus_id variant_id risk_allele risk_frequency genome_wide limited_list
<chr> <int> <chr> <chr> <dbl> <lgl> <lgl>
1 93480070 1 rs10024267 C NA FALSE FALSE
2 93480075 1 rs200854727 C NA FALSE FALSE
3 6074 1 rs1333049 C NA NA NA
4 6076 1 rs688034 T NA NA NA
5 6077 1 rs8055236 G NA NA NA
6 6075 1 rs17672135 T NA NA NA
7 23207 1 rs9349379 G NA NA NA
8 23208 1 rs12524865 C NA NA NA
9 22536 1 rs2123536 T NA NA NA
10 22537 1 rs1842896 T NA NA NA
# … with 2,778 more rows
# ℹ Use `print(n = ...)` to see more rows
Hi Ramiro thanks for the speedy reply, with warnings on it told me the SNPs. It was only a small number of them. Thank you, the package is very helpful
Hi, thank you for the useful package. When I run
get_associations()
for some SNPs (submitting one SNP at a time, but many in a row, in a for loop), I get an error 500. It seems this is when the request is too large. Do you have any suggestions? Is is possible to return an error file giving me the variant_id which produced the 500 response? Thank you