From 89f00738caa58ed2cfc8a2f4a06d6293b1227c0d Mon Sep 17 00:00:00 2001
From: Vincent LAVILLE <vincent.laville@pasteur.fr>
Date: Fri, 11 Jan 2019 12:38:03 +0100
Subject: [PATCH] Update correlationMatrix.R - Handling NAs
---
R/correlationMatrix.R | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/R/correlationMatrix.R b/R/correlationMatrix.R
index f58a981..fd6a9cd 100644
--- a/R/correlationMatrix.R
+++ b/R/correlationMatrix.R
@@ -147,6 +147,18 @@ getGenoCorMatrix <- function(lrsid, lchr, lpos, lrefall, pop, path = NULL, web =
testMat <- testMat[-to_remove, ]
genoMap <- genoMap[-to_remove,]
}
+ to_remove <- NULL
+ for (i in 1:length(lrsid)) {
+ if (!(lrsid[i] %in% rownames(testMat))) {
+ to_remove <- c(to_remove, i)
+ }
+ }
+ if (!is.null(to_remove)) {
+ lrsid <- lrsid[-to_remove]
+ lpos <- lpos[-to_remove]
+ lchr <- lchr[-to_remove]
+ lrefall <- lrefall[-to_remove]
+ }
testMat <- changeCoding(testMat, as.character(lrefall) == genoMap$REF)
colnames(testMat) <- lind
cormat = stats::cor(t(testMat))
--
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