Nothing

```
## Create basic example data frame to check Zbeta with. 15 SNPs over 5 chromosomes.
df<-data.frame(
SNP=c("SNP1","SNP2","SNP3","SNP4","SNP5","SNP6","SNP7","SNP8","SNP9","SNP10","SNP11","SNP12","SNP13","SNP14","SNP15"),
POS=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
C1=c(1,1,2,1,2,1,1,2,1,2,1,2,1,1,1),
C2=c(2,2,1,2,1,2,1,2,2,2,1,2,1,1,2),
C3=c(2,1,2,2,2,1,1,2,2,1,2,2,1,1,2),
C4=c(1,1,2,1,2,2,1,1,1,1,1,2,2,2,2),
C5=c(1,1,2,1,2,1,2,1,1,1,1,1,2,1,1)
)
## test that Zbeta is calculated correctly
test_that("Zbeta calculates Zbeta statistic correctly", {
expect_equal(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
Zbeta=c(NA,NA,NA,NA,
(10+5/18)/40,
(10+35/36)/45,
(11+103/144)/48,
(12+73/144)/49,
(11+83/144)/48,
(11+17/48)/45,
(10+65/144)/40,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with a different window size
test_that("Zbeta calculates Zbeta statistic correctly with a different window size", {
expect_equal(Zbeta(pos = df$POS, ws = 1100, x = as.matrix(df[,3:7]), 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=c(NA,NA,NA,NA,NA,
(7+11/72)/25,
(5+5/9)/25,
(6+41/144)/25,
(6+101/144)/25,
(7+17/144)/25,
NA,NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with a character matrix as x
test_that("Zbeta calculates Zbeta statistic correctly with character matrix", {
df1<-df
df1[df1==1]<-"A"
df1[df1==2]<-"B"
expect_equal(Zbeta(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), minRandL = 4, minRL = 25, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
Zbeta=c(NA,NA,NA,NA,
(10+5/18)/40,
(10+35/36)/45,
(11+103/144)/48,
(12+73/144)/49,
(11+83/144)/48,
(11+17/48)/45,
(10+65/144)/40,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with X supplied as a parameter
test_that("Zbeta calculates Zbeta statistic correctly with X supplied", {
expect_equal(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = c(700,900)),
list(
position=c(700,800,900),
Zbeta=c((11+103/144)/48,
(12+73/144)/49,
(11+83/144)/48)
),tolerance=0.0001)
})
## Test the function with X supplied as a parameter outside of the region defined in pos
test_that("Zbeta fails with an X supplied outside of the region defined in pos", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = c(7000,9000)),
"The region specified by X is outside the region contained in the pos vector")
})
## Test the function with X supplied as character
test_that("Zbeta fails with an X supplied as a character", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = c("700bp","900bp")),
"X should be a numeric vector of length 2 e.g. c(100,200)",
fixed=TRUE)
})
## Test the function with X supplied as only one number
test_that("Zbeta fails with an X supplied as only one number", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = 700),
"X should be a numeric vector of length 2 e.g. c(100,200)",
fixed=TRUE)
})
## Test the function with X supplied with too many numbers
test_that("Zbeta fails with an X supplied with too many numbers", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = c(700,900,1100)),
"X should be a numeric vector of length 2 e.g. c(100,200)",
fixed=TRUE)
})
## Test the function with ws non-numeric
test_that("Zbeta fails when ws is non-numeric", {
expect_error(Zbeta(pos = df$POS, ws = "3000bp", x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = NULL),
"ws must be a number greater than 0")
})
## Test the function with ws = 0
test_that("Zbeta fails when ws is zero", {
expect_error(Zbeta(pos = df$POS, ws = 0, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = NULL),
"ws must be a number greater than 0")
})
## Test the function with positions non-numeric
test_that("Zbeta fails when pos is non-numeric", {
expect_error(Zbeta(pos = paste0(df$POS,"bp"), ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 25, X = NULL),
"pos must be a numeric vector")
})
## Test the function with minLandR as non-numeric
test_that("Zbeta fails when minLandR is non-numeric", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = "4snps", minRL = 25, X = NULL),
"minRandL must be a number greater than or equal to 0")
})
## Test the function with minLandR as negative
test_that("Zbeta fails when minLandR is negative", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = -1, minRL = 25, X = NULL),
"minRandL must be a number greater than or equal to 0")
})
## Test the function with minLR as non-numeric
test_that("Zbeta fails when minLR is non-numeric", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = "25b", X = NULL),
"minRL must be a number greater than or equal to 0")
})
## Test the function with minLR as negative
test_that("Zbeta fails when minLR is negative", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = -25, X = NULL),
"minRL must be a number greater than or equal to 0")
})
## Test the function with x not a matrix
test_that("Zbeta fails when x is not a matrix", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = df[,3:7], minRandL = 4, minRL = 25, X = NULL),
"x must be a matrix")
})
## Test the function with x not having the correct amount of rows
test_that("Zbeta fails when the number of rows in x is not equal to the length of pos", {
expect_error(Zbeta(pos = df$POS, ws = 3000, x = t(as.matrix(df[,3:7])), minRandL = 4, minRL = 25, X = NULL),
"The number of rows in x must equal the number of SNP locations given in pos")
})
## Test the function with a SNP having only one allele
test_that("Zbeta fails when a SNP has only one allele", {
df1<-df
df1[1,3:7]<-1
expect_error(Zbeta(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), minRandL = 4, minRL = 25, X = NULL),
"SNPs must all be biallelic")
})
## Test the function with a SNP having more than two alleles
test_that("Zbeta fails when a SNP has more than two alleles", {
df1<-df
df1[1,7]<-3
expect_error(Zbeta(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), minRandL = 4, minRL = 25, X = NULL),
"SNPs must all be biallelic")
})
## Test the warning that all values returned are NA by increasing minRL
test_that("Zbeta warns about all NAs", {
expect_warning(Zbeta(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), minRandL = 4, minRL = 50, X = NULL),
"No Zbeta values were calculated, try reducing minRandL and minRL or increasing the window size")
})
## test that Zbeta works with a missing value
df1<-df
df1$C1[15]<-NA
test_that("Zbeta calculates Zbeta statistic correctly with missing value", {
expect_equal(Zbeta(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), 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=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)
})
```

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