diff --git a/R/extraction_1KG.R b/R/extraction_1KG.R index 4a13e6e1a76a68dd06e48eb2d4875c0854d24dbb..9cd11a6e4cdbeac409a6848e3d36a26109c40e84 100644 --- a/R/extraction_1KG.R +++ b/R/extraction_1KG.R @@ -111,8 +111,8 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) { # These are variants filtered by Brian Browning, the developer of BEAGLE. data_url = paste(sep = "", "http://tabix.iobio.io/?cmd=-h%20%27", - "http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/", - "individual_chromosomes/chr", chrom, ".1kg.phase3.v5a.vcf.gz", + "http://bochet.gcc.biostat.washington.edu/beagle/1000_Genomes_phase3_v5a/b37.vcf/", + "chr", chrom, ".1kg.phase3.v5a.vcf.gz", "%27%20", chrom, ":", start, "-", end ) # Download the data from the server. @@ -161,7 +161,7 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) { # Convert the genotypes to a numeric matrix. retval$geno <- t(apply(retval$geno, 1, function(row) { - as.numeric(do.call(cbind, strsplit(row, "|", fixed = TRUE))) + as.numeric(do.call(cbind, strsplit(unlist(row), "[/|]"))) })) rownames(retval$geno) <- retval$meta$ID