From c8dde0f03e90296d82fa148664c525d2bd010aaa Mon Sep 17 00:00:00 2001
From: Vincent LAVILLE <vincent.laville@pasteur.fr>
Date: Wed, 23 Jan 2019 13:16:34 +0100
Subject: [PATCH] Update extraction_1KG.R
---
R/extraction_1KG.R | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/R/extraction_1KG.R b/R/extraction_1KG.R
index afcaae4..cf43320 100644
--- a/R/extraction_1KG.R
+++ b/R/extraction_1KG.R
@@ -129,6 +129,9 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) {
vcf <- utils::read.delim(
text = gsub("##", "!", txt), header = TRUE, comment.char = "!", stringsAsFactors = FALSE)
+ # Discard multi-allelic markers.
+ vcf <- vcf[grep(",", vcf$ALT, invert = TRUE), ]
+
# Throw error if SNP not found
if (nrow(vcf) < 1) {
msg <- paste("SNP ", chrom, ":", start, "-", end, " not found", sep = "")
@@ -140,10 +143,7 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) {
# Assign the standard column names and sample identifiers.
colnames(vcf)[1] <- "CHROM"
- # Discard multi-allelic markers.
- vcf <- vcf[grep(",", vcf$ALT, invert = TRUE), ]
-
- # Select the genotype columns that belong to a particular population.
+ # Select the genotype columns that belong to a particular population.
if (pop %in% pops) {
vcf <- vcf[,c(rep(TRUE, 9), pops == pop)]
} else if (pop %in% superpops) {
--
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