SNP查找MAF代码

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已于 2024-01-12 15:52:34 修改

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分类专栏： MR 文章标签： chrome 前端

于 2023-09-06 15:46:07 首次发布

本文链接：https://blog.csdn.net/shuai19970911/article/details/132717002

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library(httr)
library(jsonlite)
library(xml2)
server <- "http://grch37.rest.ensembl.org"


for (m in exposure$SNP) {

path1 = paste0("/variation/human/", m, '?pops=1')
ext <- path1

res <- GET(paste(server, ext, sep = ""), content_type("application/json"))

stop_for_status(res)

res <- httr::content(res)
res <- jsonlite::fromJSON(toJSON(res))$populations
s = res[res$population == '1000GENOMES:phase_3:EUR',]
s_res = s[s$allele == exposure[exposure$SNP == m,"effect_allele.exposure"],]
exposure[exposure$SNP == m, ]$eaf.exposure = s_res$frequency
print(s_res)
}