PheWAS / GWAS lead variants & Tag variants query for multiple snps

Data Access GraphQL API
1

Dear Open Targets Team,

First of all thank you very much for this very useful tool, I’m a big fan.

I am trying to query the following tables for multiples snps:

  1. PheWAS
  2. GWAS lead variants
  3. Tag variants

For PheWAS I am using this code in R:

library(httr)
library(rlist)
library(dplyr)

Build query string

query_string = "
query PheWASQuery{
pheWAS($variantId: String!) {
associations {
study {
studyId
traitReported
traitCategory
pmid
pubDate
pubAuthor
source
}
pval
beta
oddsRatio
nTotal
nCases
eaf
se
}
}
}"

Set base URL of GraphQL API endpoint

base_url ← “https://api.genetics.opentargets.org/graphql”

Set gene_id variable

variantId<-“1_154453788_C_T”

for (i in variantId) {

Set variables object of arguments to be passed to endpoint

variables ← list(“variantId” = i)

Construct POST request body object with query string and variables

post_body ← list(query = query_string, variables = variables)

Perform POST request

r ← POST(url=base_url, body=post_body, encode=‘json’)

df = content(r)

Flatten the nested result fields into a dataframe

list_result = content(r)$data$locations
x = lapply(list_result, list.flatten)

result = bind_rows(x)}

But when I do content(r) I get:

$syntaxError
[1] “Syntax error while parsing GraphQL query. Invalid input "query PheWASQuery{\n pheWAS($", expected ExecutableDefinition or TypeSystemDefinition (line 2, column 1):\nquery PheWASQuery{\n^”

$locations
$locations[[1]]
$locations[[1]]$line
[1] 2

$locations[[1]]$column
[1] 1

I’d really appreciate if you could assist me in how to correct my code.
I also would like to adapt the code to obtain this two other tables:

  • GWAS lead variants
  • Tag variants

Any help would be much appreciated!! Many thanks!

Paloma

2

It’s complaining about your query. There are some issues with the structure of the query (e.g. studyId )

You can try to debug the issue using the GraphQL browser