slowkow
commented
3 years ago Please try an alternative.
Alternative 1: LDproxy
https://ldlink.nci.nih.gov/?tab=ldproxy
Alternative 2: Ensembl
http://grch37.rest.ensembl.org/documentation/info/ld_region_get
Computes and returns LD values between all pairs of variants in the defined region.
http://grch37.rest.ensembl.org/documentation/info/ld_id_get
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
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