From 138ce99c639c78a609eaabf290a8d83b3815c5b0 Mon Sep 17 00:00:00 2001
From: Clare <chorscroft@users.noreply.github.com>
Date: Tue, 8 Sep 2020 21:31:35 +0100
Subject: [PATCH] Chnage to L_plus_R so that it will return zero rather than NA
when n<2 in choose(n,2)
---
R/L_plus_R.R | 7 ++-----
tests/testthat/test-L_plus_R.R | 4 ++--
2 files changed, 4 insertions(+), 7 deletions(-)
diff --git a/R/L_plus_R.R b/R/L_plus_R.R
index 848b6b2..70316df 100644
--- a/R/L_plus_R.R
+++ b/R/L_plus_R.R
@@ -66,11 +66,8 @@ L_plus_R <- function(pos, ws, X = NULL) {
## get L, R and L_plus_R
noL <- length(pos[pos>=currentPos-ws/2 & pos < currentPos]) ## Number of SNPs to the left of the current SNP
noR <- length(pos[pos<=currentPos+ws/2 & pos > currentPos]) ## Number of SNPs to the right of the current SNP
- if(noL < 2 || noR < 2){ #Must be at least 2 to calculate n choose 2
- outputList$L_plus_R[i]<-NA
- } else {
- outputList$L_plus_R[i]<-choose(noL,2)+choose(noR,2)
- }
+ ## if n < 2 then choose function will return 0
+ outputList$L_plus_R[i]<-choose(noL,2)+choose(noR,2)
}
return(outputList)
}
diff --git a/tests/testthat/test-L_plus_R.R b/tests/testthat/test-L_plus_R.R
index 3680384..2e02d9e 100644
--- a/tests/testthat/test-L_plus_R.R
+++ b/tests/testthat/test-L_plus_R.R
@@ -12,7 +12,7 @@ test_that("L_plus_R calculates L_plus_R statistic correctly", {
expect_equal(L_plus_R(pos = df$POS, ws = 3000, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
- L_plus_R=c(NA,NA,67,58,51,46,43,42,43,46,51,58,67,NA,NA)
+ L_plus_R=c(91,78,67,58,51,46,43,42,43,46,51,58,67,78,91)
))
})
@@ -23,7 +23,7 @@ test_that("L_plus_R calculates L_plus_R statistic correctly with a different win
expect_equal(L_plus_R(pos = df$POS, ws = 1100, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
- L_plus_R=c(NA,NA,11,13,16,20,20,20,20,20,16,13,11,NA,NA)
+ L_plus_R=c(10,10,11,13,16,20,20,20,20,20,16,13,11,10,10)
))
})
--
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