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This repository has been archived by the owner on Mar 10, 2023. It is now read-only.
Computes and returns LD values between the given variant and all other variants in a window centered around the given variant. The window size is set to 500 kb.
Example code:
library(httr)
library(jsonlite)
library(xml2)
server<-"http://grch37.rest.ensembl.org"ext<-"/ld/human/rs42/1000GENOMES:phase_3:EUR"r<- GET(paste(server, ext, sep=""), content_type("application/json"))
stop_for_status(r)
# use this if you get a simple nested list back, otherwise inspect its structure# head(data.frame(t(sapply(content(r),c))))
head(fromJSON(toJSON(content(r))))
#> population_name r2 d_prime variation1 variation2#> 1 1000GENOMES:phase_3:EUR 0.060888 0.790030 rs42 rs12699249#> 2 1000GENOMES:phase_3:EUR 0.147759 0.861987 rs42 rs17633604#> 3 1000GENOMES:phase_3:EUR 0.128357 0.781375 rs42 rs10486144#> 4 1000GENOMES:phase_3:EUR 0.334122 0.936431 rs42 rs29#> 5 1000GENOMES:phase_3:EUR 0.060888 0.790030 rs42 rs12699248#> 6 1000GENOMES:phase_3:EUR 0.629504 0.978462 rs42 rs15
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Hi,
I am getting this error...
... when running this code:
d <- get_proxies(chrom = "12", pos = 583090, window_size = 1e5, pop = "AFR")
How can I fix this?
Best,
Sander
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