Source files lost?

[TaruMuranen]

2018-04-25 14.15 EEST running: d <- get_proxies(chrom = "12", pos = 583090, window_size = 1e5, pop = "AFR") gives error message: Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input

get_proxies() worked all right about 24h earlier.

[mreppell]

They seem to have moved to: http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/vcf.b37/

When I went in to debug in the get_proxies function and substituted that for the current url: http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/individual_chromosomes/

The package would work again

[slowkow]

@TaruMuranen Thanks for reporting this issue!

@mreppell Thanks for pointing out the fix!

Here's an example I tried to test if it is working after changing the BEAGLE URL:

library(proxysnps)
d <- get_proxies(chrom = "12", pos = 583090, window_size = 1e5, pop = "AFR")
head(d)

    CHROM    POS          ID REF ALT   ALT_FREQ        R R.squared  D.prime CHOSEN
663    12 583090  rs11063140   A   G 0.15506808 1.000000  1.000000 1.000000   TRUE
685    12 584423  rs10849066   A   G 0.23071104 0.772357  0.596535 0.987318  FALSE
661    12 583003  rs11063139   C   T 0.16868381 0.738975  0.546084 0.777021  FALSE
678    12 584054 rs145345255   G   A 0.07791225 0.655136  0.429203 0.965528  FALSE
682    12 584354  rs10849065   G   T 0.18759455 0.613153  0.375957 0.687769  FALSE
711    12 586815  rs58254236   C   T 0.08396369 0.601214  0.361458 0.850726  FALSE

plot(d$POS, d$R.squared, main="rs11063140", xlab="Position", ylab=bquote("R"^2))

Please try re-installing the package:

devtools::install_github("slowkow/proxysnps")

[seafloor]

Just to add that I got the same error when the files got moved, and that the latest commit solved the issue. Thanks for the quick fix!