From cec668788e94cc416ef060d33ca83e9da305f220 Mon Sep 17 00:00:00 2001
From: Vincent LAVILLE <vincent.laville@pasteur.fr>
Date: Thu, 10 Jan 2019 13:04:07 +0100
Subject: [PATCH] Update url and fix bugs
---
R/extraction_1KG.R | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/R/extraction_1KG.R b/R/extraction_1KG.R
index 4a13e6e..9cd11a6 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
--
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