英文:
How to run a AR query for multiple arguments of a table or list (lets say we have a column with IDs) in R
问题
Install relevant library for HTTP requests
library(httr)
Set gene_id variable for AR (androgen receptor)
gene_id <- "ENSG00000169083"
Build query string to get general information about AR and genetic constraint and tractability assessments
query_string = "
query target($ensemblId: String!){
target(ensemblId: $ensemblId){
id
approvedSymbol
biotype
geneticConstraint {
constraintType
exp
obs
score
oe
oeLower
oeUpper
}
tractability {
id
modality
value
}
}
}
"
Set base URL of GraphQL API endpoint
base_url <- "https://api.platform.opentargets.org/api/v4/graphql"
Set variables object of arguments to be passed to endpoint
variables <- list("ensemblId" = gene_id)
Construct POST request body object with query string and variables
post_body <- list(query = query_string, variables = variables)
Perform POST request
r <- POST(url=base_url, body=post_body, encode='json')
Print data to RStudio console
print(content(r)$data)
英文:
How to modify this script to read form a list of IDs and return the results ?
# Install relevant library for HTTP requestslibrary(httr)# Set gene_id variable for AR (androgen receptor)gene_id <- "ENSG00000169083"# Build query string to get general information about AR and genetic constraint and tractability assessmentsquery_string = "query target($ensemblId: String!){target(ensemblId: $ensemblId){idapprovedSymbolbiotypegeneticConstraint {constraintTypeexpobsscoreoeoeLoweroeUpper}tractability {idmodalityvalue}}}"# Set base URL of GraphQL API endpointbase_url <- "https://api.platform.opentargets.org/api/v4/graphql"# Set variables object of arguments to be passed to endpointvariables <- list("ensemblId" = gene_id)# Construct POST request body object with query string and variablespost_body <- list(query = query_string, variables = variables)# Perform POST requestr <- POST(url=base_url, body=post_body, encode='json')# Print data to RStudio consoleprint(content(r)$data)
I tried just a simple query from the documentation of Open Targets. Their graphQL API doesn't support multiple IDs.
答案1
得分: 0
遍历多个 ID 可能会像这样完成：
IDs <- c("ENSG00000169083", "ENSG00000169084", ...)alldata <- lapply(IDs, function(gene_id) {post_body <- list(query = query_string, variables = list("ensemblId" = gene_id))res <- tryCatch(POST(url=base_url, body=post_body, encode='json'),error = function(e) e)if (inherits(res, "error")) {warning("基因", sQuote(gene_id, FALSE), "出错: ",conditionMessage(res), call. = FALSE)res <- NULL} else if (status_code(res) != 200) {warning("基因", sQuote(gene_id, FALSE), "返回异常: ",status_code(res), call. = FALSE)res <- NULL} else {res <- content(res)$data}res})
从这里开始，你应该有一个包含每个 ID 一个元素的列表，然后你可以组合数据（使用 rbind、bind_rows、rbindlist，或者可能使用一些特定于列表的方法）。
英文:
Iterating over multiple IDs might be done like this:
IDs <- c("ENSG00000169083", "ENSG00000169084", ...)alldata <- lapply(IDs, function(gene_id) {post_body <- list(query = query_string, variables = list("ensemblId" = gene_id))res <- tryCatch(POST(url=base_url, body=post_body, encode='json'),error = function(e) e)if (inherits(res, "error")) {warning("error for gene ", sQuote(gene_id, FALSE), ": ",conditionMessage(res), call. = FALSE)res <- NULL} else if (status_code(res) != 200) {warning("abnormal return for gene ", sQuote(gene_id, FALSE), ": ",status_code(res), call. = FALSE)res <- NULL} else {res <- content(res)$data}res})
From here, you should have a list with one element per ID, over to you on combining the data (whether rbind, bind_rows, rbindlist, or something list-specific perhaps).
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