From eddb955be56cd1452748d38f9c6440def479e80c Mon Sep 17 00:00:00 2001
From: Clare <chorscroft@users.noreply.github.com>
Date: Tue, 15 Sep 2020 09:03:04 +0100
Subject: [PATCH] Added test for when a pair of SNPs in a window have a genetic
distance greater than the maximum bin in the LD profile
---
tests/testthat/test-Zalpha_BetaCDF.R | 21 +++++++++++++++
tests/testthat/test-Zalpha_Zscore.R | 22 ++++++++++++++++
tests/testthat/test-Zalpha_all.R | 26 +++++++++++++++++++
tests/testthat/test-Zalpha_expected.R | 21 +++++++++++++++
.../test-Zalpha_log_rsq_over_expected.R | 21 +++++++++++++++
.../testthat/test-Zalpha_rsq_over_expected.R | 21 +++++++++++++++
tests/testthat/test-Zbeta_BetaCDF.R | 21 +++++++++++++++
tests/testthat/test-Zbeta_Zscore.R | 21 +++++++++++++++
tests/testthat/test-Zbeta_expected.R | 22 ++++++++++++++++
.../test-Zbeta_log_rsq_over_expected.R | 21 +++++++++++++++
tests/testthat/test-Zbeta_rsq_over_expected.R | 21 +++++++++++++++
11 files changed, 238 insertions(+)
diff --git a/tests/testthat/test-Zalpha_BetaCDF.R b/tests/testthat/test-Zalpha_BetaCDF.R
index 81f6b27..ddc5f3d 100644
--- a/tests/testthat/test-Zalpha_BetaCDF.R
+++ b/tests/testthat/test-Zalpha_BetaCDF.R
@@ -332,3 +332,24 @@ test_that("Zalpha_BetaCDF calculates Zalpha_BetaCDF statistic correctly with mis
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zalpha_BetaCDF calculates Zalpha_BetaCDF statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zalpha_BetaCDF(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_Beta_a = LDprofile$Beta_a, LDprofile_Beta_b = LDprofile$Beta_b, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zalpha_BetaCDF=c(NA,NA,NA,NA,
+ 0.528754272440162,
+ 0.554657151730784,
+ 0.490365350771199,
+ 0.429958093556324,
+ 0.388665184297966,
+ 0.396797658473664,
+ 0.40379809759356,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zalpha_Zscore.R b/tests/testthat/test-Zalpha_Zscore.R
index a018afa..5fb03f1 100644
--- a/tests/testthat/test-Zalpha_Zscore.R
+++ b/tests/testthat/test-Zalpha_Zscore.R
@@ -351,3 +351,25 @@ test_that("Zalpha_Zscore calculates Zalpha_Zscore statistic correctly with missi
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zalpha_Zscore calculates Zalpha_Zscore statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zalpha_Zscore(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, LDprofile_sd = LDprofile$sd, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zalpha_Zscore=c(NA,NA,NA,NA,
+ 0.171551248775495,
+ 0.250751380960093,
+ 0.0418726269555867,
+ -0.192722802223301,
+ -0.316679396412605,
+ -0.285401890619276,
+ -0.244931914193891,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
+
diff --git a/tests/testthat/test-Zalpha_all.R b/tests/testthat/test-Zalpha_all.R
index 8240dbf..6c6bd0f 100644
--- a/tests/testthat/test-Zalpha_all.R
+++ b/tests/testthat/test-Zalpha_all.R
@@ -568,3 +568,29 @@ test_that("Zalpha_all calculates statistics correctly with missing value", {
Zbeta=c(NA,NA,NA,NA,0.248611111111111,0.235185185185185,0.233651620370370,0.257794784580499,0.250144675925926,0.259413580246914,0.271354166666667,NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zalpha_all calculates statistics correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zalpha_all(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, LDprofile_sd = LDprofile$sd, LDprofile_Beta_a = LDprofile$Beta_a, LDprofile_Beta_b = LDprofile$Beta_b, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ LR=c(0,13,24,33,40,45,48,49,48,45,40,33,24,13,0),
+ L_plus_R=c(91,78,67,58,51,46,43,42,43,46,51,58,67,78,91),
+ Zalpha_expected=c(NA, NA, NA, NA, 0.35775270849344, 0.360194100145564, 0.36882454832507, 0.379040922949242, 0.400715520018796, 0.401718327864356, 0.388093039845692, NA, NA, NA, NA),
+ Zbeta_expected=c(NA, NA, NA, NA, 0.309796639287645, 0.306356600239621, 0.299229117644403, 0.287619092597206, 0.271195118636169, 0.271195118636169, 0.285239698673566, NA, NA, NA, NA),
+ Zalpha=c(NA, NA, NA, NA, 0.417052469135803, 0.449363425925926, 0.377521494708995, 0.298941798941799, 0.270709325396825, 0.281925154320988, 0.287615740740741, NA, NA, NA, NA),
+ Zbeta=c(NA, NA, NA, NA, 0.256944444444444, 0.243827160493827, 0.244068287037037, 0.255243764172336, 0.241174768518518, 0.252314814814815, 0.261284722222222, NA, NA, NA, NA),
+ Zalpha_rsq_over_expected=c(NA, NA, NA, NA, 1.19167472080619, 1.27358283231798, 1.05911709750039, 0.813967663774974, 0.691051112331195, 0.728230393808371, 0.76047497606951, NA, NA, NA, NA),
+ Zalpha_log_rsq_over_expected=c(NA, NA, NA, NA, -0.0866699301333792, -0.0450984996562888, -0.170082829057599, -0.292011096473854, -0.355497049708911, -0.345346264723395, -0.325460796768333, NA, NA, NA, NA),
+ Zbeta_rsq_over_expected=c(NA, NA, NA, NA, 0.829165822709247, 0.794411354588777, 0.811051641594364, 0.879635831191311, 0.8893035012259, 0.93038110746129, 0.936927121826222, NA, NA, NA, NA),
+ Zbeta_log_rsq_over_expected=c(NA, NA, NA, NA, -0.253507645357523, -0.252472151393989, -0.264919235707824, -0.237790197768511, -0.231067956739982, -0.186686780456914, -0.194302291843375, NA, NA, NA, NA),
+ Zalpha_Zscore=c(NA, NA, NA, NA, 0.171551248775495, 0.250751380960093, 0.0418726269555867, -0.192722802223301, -0.316679396412605, -0.285401890619276, -0.244931914193891, NA, NA, NA, NA),
+ Zbeta_Zscore=c(NA, NA, NA, NA, -0.155023529432353, -0.185399969976716, -0.168250652582989, -0.104627764295373, -0.0955723675990356, -0.0601070717071691, -0.0618178441622676, NA, NA, NA, NA),
+ Zalpha_BetaCDF=c(NA, NA, NA, NA, 0.528754272440162, 0.554657151730784, 0.490365350771199, 0.429958093556324, 0.388665184297966, 0.396797658473664, 0.40379809759356, NA, NA, NA, NA),
+ Zbeta_BetaCDF=c(NA, NA, NA, NA, 0.459559291673423, 0.456100842212321, 0.459910029690557, 0.479549830626744, 0.482519290259401, 0.49506531210108, 0.488097958454476, NA, NA, NA, NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zalpha_expected.R b/tests/testthat/test-Zalpha_expected.R
index 635c5fe..90b77b8 100644
--- a/tests/testthat/test-Zalpha_expected.R
+++ b/tests/testthat/test-Zalpha_expected.R
@@ -247,3 +247,24 @@ test_that("Zalpha_expected fails when LDprofile_bins and LDprofile_rsq are diffe
expect_error(Zalpha_expected(pos = df$POS, ws = 3000, dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = c(LDprofile$rsq,1), minRandL = 4, minRL = 25, X = NULL),
"LDprofile_rsq must contain the same number of values as there are bins given in LDprofile_bins")
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zalpha_expected calculates Zalpha_expected statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zalpha_expected(pos = df1$POS, ws = 3000, dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zalpha_expected=c(NA,NA,NA,NA,
+ 0.35775270849344,
+ 0.360194100145564,
+ 0.36882454832507,
+ 0.379040922949242,
+ 0.400715520018796,
+ 0.401718327864356,
+ 0.388093039845692,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zalpha_log_rsq_over_expected.R b/tests/testthat/test-Zalpha_log_rsq_over_expected.R
index b05466d..d88cec7 100644
--- a/tests/testthat/test-Zalpha_log_rsq_over_expected.R
+++ b/tests/testthat/test-Zalpha_log_rsq_over_expected.R
@@ -325,3 +325,24 @@ test_that("Zalpha_log_rsq_over_expected calculates Zalpha_log_rsq_over_expected
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zalpha_log_rsq_over_expected calculates Zalpha_log_rsq_over_expected statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zalpha_log_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zalpha_log_rsq_over_expected=c(NA,NA,NA,NA,
+ -0.0866699301333792,
+ -0.0450984996562888,
+ -0.170082829057599,
+ -0.292011096473854,
+ -0.355497049708911,
+ -0.345346264723395,
+ -0.325460796768333,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zalpha_rsq_over_expected.R b/tests/testthat/test-Zalpha_rsq_over_expected.R
index 634c5ff..bc9d2e4 100644
--- a/tests/testthat/test-Zalpha_rsq_over_expected.R
+++ b/tests/testthat/test-Zalpha_rsq_over_expected.R
@@ -325,3 +325,24 @@ test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statisti
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zalpha_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zalpha_rsq_over_expected=c(NA,NA,NA,NA,
+ 1.19167472080619,
+ 1.27358283231798,
+ 1.05911709750039,
+ 0.813967663774974,
+ 0.691051112331195,
+ 0.728230393808371,
+ 0.76047497606951,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zbeta_BetaCDF.R b/tests/testthat/test-Zbeta_BetaCDF.R
index 580d35e..079cf9b 100644
--- a/tests/testthat/test-Zbeta_BetaCDF.R
+++ b/tests/testthat/test-Zbeta_BetaCDF.R
@@ -332,3 +332,24 @@ test_that("Zbeta_BetaCDF calculates Zbeta_BetaCDF statistic correctly with missi
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zbeta_BetaCDF calculates Zbeta_BetaCDF statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zbeta_BetaCDF(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_Beta_a = LDprofile$Beta_a, LDprofile_Beta_b = LDprofile$Beta_b, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zbeta_BetaCDF=c(NA,NA,NA,NA,
+ 0.459559291673423,
+ 0.456100842212321,
+ 0.459910029690557,
+ 0.479549830626744,
+ 0.482519290259401,
+ 0.49506531210108,
+ 0.488097958454476,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zbeta_Zscore.R b/tests/testthat/test-Zbeta_Zscore.R
index b1ef29d..6d940da 100644
--- a/tests/testthat/test-Zbeta_Zscore.R
+++ b/tests/testthat/test-Zbeta_Zscore.R
@@ -351,3 +351,24 @@ test_that("Zbeta_Zscore calculates Zbeta_Zscore statistic correctly with missing
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zbeta_Zscore calculates Zbeta_Zscore statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zbeta_Zscore(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, LDprofile_sd = LDprofile$sd, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zbeta_Zscore=c(NA,NA,NA,NA,
+ -0.155023529432353,
+ -0.185399969976716,
+ -0.168250652582989,
+ -0.104627764295373,
+ -0.0955723675990356,
+ -0.0601070717071691,
+ -0.0618178441622676,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zbeta_expected.R b/tests/testthat/test-Zbeta_expected.R
index 8a499b8..6dce102 100644
--- a/tests/testthat/test-Zbeta_expected.R
+++ b/tests/testthat/test-Zbeta_expected.R
@@ -247,3 +247,25 @@ test_that("Zbeta_expected fails when LDprofile_bins and LDprofile_rsq are differ
expect_error(Zbeta_expected(pos = df$POS, ws = 3000, dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = c(LDprofile$rsq,1), minRandL = 4, minRL = 25, X = NULL),
"LDprofile_rsq must contain the same number of values as there are bins given in LDprofile_bins")
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zbeta_expected calculates Zbeta_expected statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zbeta_expected(pos = df1$POS, ws = 3000, dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zbeta_expected=c(NA,NA,NA,NA,
+ 0.309796639287645,
+ 0.306356600239621,
+ 0.299229117644403,
+ 0.287619092597206,
+ 0.271195118636169,
+ 0.271195118636169,
+ 0.285239698673566,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
+
diff --git a/tests/testthat/test-Zbeta_log_rsq_over_expected.R b/tests/testthat/test-Zbeta_log_rsq_over_expected.R
index d7f841e..cc50f4d 100644
--- a/tests/testthat/test-Zbeta_log_rsq_over_expected.R
+++ b/tests/testthat/test-Zbeta_log_rsq_over_expected.R
@@ -325,3 +325,24 @@ test_that("Zbeta_log_rsq_over_expected calculates Zbeta_log_rsq_over_expected st
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zbeta_log_rsq_over_expected calculates Zbeta_log_rsq_over_expected statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zbeta_log_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zbeta_log_rsq_over_expected=c(NA,NA,NA,NA,
+ -0.253507645357523,
+ -0.252472151393989,
+ -0.264919235707824,
+ -0.237790197768511,
+ -0.231067956739982,
+ -0.186686780456914,
+ -0.194302291843375,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
diff --git a/tests/testthat/test-Zbeta_rsq_over_expected.R b/tests/testthat/test-Zbeta_rsq_over_expected.R
index 5020ba4..74438ef 100644
--- a/tests/testthat/test-Zbeta_rsq_over_expected.R
+++ b/tests/testthat/test-Zbeta_rsq_over_expected.R
@@ -325,3 +325,24 @@ test_that("Zbeta_rsq_over_expected calculates Zbeta_rsq_over_expected statistic
NA,NA,NA,NA)
),tolerance=0.0001)
})
+
+## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
+
+df1<-df
+df1$dist[10:15]<-df1$dist[10:15]+0.1
+test_that("Zbeta_rsq_over_expected calculates Zbeta_rsq_over_expected statistic correctly when biggest bin is bigger than LDprofile", {
+
+ expect_equal(Zbeta_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
+ list(
+ position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
+ Zbeta_rsq_over_expected=c(NA,NA,NA,NA,
+ 0.829165822709247,
+ 0.794411354588777,
+ 0.811051641594364,
+ 0.879635831191311,
+ 0.8893035012259,
+ 0.93038110746129,
+ 0.936927121826222,
+ NA,NA,NA,NA)
+ ),tolerance=0.0001)
+})
--
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