Nothing
tests/testthat/test-Zalpha_rsq_over_expected.R
In zalpha: Run a Suite of Selection Statistics
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),
dist=c(0,0.00101,0.00123,0.00207,0.00218,0.00223,0.00235,0.00251,0.00272,0.00289,0.00304,0.00316,0.00335,0.00345,0.00374)
)
LDprofile<-data.frame(
bin=seq(0,0.0049,0.0001),
rsq=c(0.495714059385946,0.411014233619574,0.395532914859378,0.44354526861954,0.435550945945946,
0.419534577303153,0.383410708498866,0.402439897670834,0.395945237932081,0.380436909495495,
0.384229510773621,0.379494011054621,0.368118044626627,0.358753523652643,0.362330915047976,
0.372142680938693,0.353703415234045,0.341173431307316,0.345578512726934,0.358159779825909,
0.334687181997538,0.337442516960342,0.343721563062338,0.336509253287721,0.325271170690837,
0.325488235114597,0.32078065970396,0.317594707821212,0.314613974963111,0.309774332543378,
0.307619999017408,0.307004105181405,0.300279349768979,0.305505356875903,0.303179706053309,
0.312783673753436,0.308540965611869,0.292690196360757,0.299428992380521,0.297144304197462,
0.286701832971995,0.297894654636997,0.283984127549023,0.283253709389766,0.281330372503553,
0.289052362087009,0.272730959781483,0.277399161038311,0.285764741944136,0.271195118636169)
)
## test that Zalpha_rsq_over_expected is calculated correctly
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly", {
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$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,
1.099392777415350,
1.175423932431810,
0.973208670564282,
0.767152145198758,
0.691051112331195,
0.728230393808371,
0.737847444047460,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with a different window size
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with a different window size", {
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 1100, x = as.matrix(df[,3:7]), dist = df$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,NA,
1.120554321638970,
0.961086582792753,
0.658704548108426,
0.499640647493653,
0.478776705516631,
NA,NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with a character matrix as x
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with character matrix", {
df1<-df
df1[df1==1]<-"A"
df1[df1==2]<-"B"
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df$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,
1.099392777415350,
1.175423932431810,
0.973208670564282,
0.767152145198758,
0.691051112331195,
0.728230393808371,
0.737847444047460,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with X supplied as a parameter
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with X supplied", {
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = c(700,900)),
list(
position=c(700,800,900),
Zalpha_rsq_over_expected=c(0.973208670564282,
0.767152145198758,
0.691051112331195)
),tolerance=0.0001)
})
## Test the function with X supplied as a parameter outside of the region defined in pos
test_that("Zalpha_rsq_over_expected fails with an X supplied outside of the region defined in pos", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails with an X supplied as a character", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails with an X supplied as only one number", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails with an X supplied with too many numbers", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails when ws is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = "3000bp", x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"ws must be a number greater than 0")
})
## Test the function with ws = 0
test_that("Zalpha_rsq_over_expected fails when ws is zero", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 0, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"ws must be a number greater than 0")
})
## Test the function with positions non-numeric
test_that("Zalpha_rsq_over_expected fails when pos is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = paste0(df$POS,"bp"), ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"pos must be a numeric vector")
})
## Test the function with minLandR as non-numeric
test_that("Zalpha_rsq_over_expected fails when minLandR is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails when minLandR is negative", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails when minLR is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails when minLR is negative", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = -25, X = NULL),
"minRL must be a number greater than or equal to 0")
})
## Test the warning that all values returned are NA by increasing minRL
test_that("Zalpha_rsq_over_expected warns about all NAs", {
expect_warning(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 50, X = NULL),
"No Zalpha_rsq_over_expected values were calculated, try reducing minRandL and minRL or increasing the window size")
})
## Test the function with dists non-numeric
test_that("Zalpha_rsq_over_expected fails when dist is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = paste0(df$dist,"dist"), LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"dist must be a numeric vector")
})
## Test the function with dists a different length to pos
test_that("Zalpha_rsq_over_expected fails when dist is a different length to pos", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = c(df$dist,1), LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"The number of values in dist must equal the number of SNP locations given in pos")
})
## Test the function with LDprofile_bins non-numeric
test_that("Zalpha_rsq_over_expected fails when LDprofile_bins is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = paste0(LDprofile$bin,"dist"), LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"LDprofile_bins must be a numeric vector")
})
## Test the function with LDprofile_bins not of equal size
tempLDprofile<-data.frame(
bin=c(seq(0,0.0048,0.0001),3),
rsq=c(0.495714059385946,0.411014233619574,0.395532914859378,0.44354526861954,0.435550945945946,
0.419534577303153,0.383410708498866,0.402439897670834,0.395945237932081,0.380436909495495,
0.384229510773621,0.379494011054621,0.368118044626627,0.358753523652643,0.362330915047976,
0.372142680938693,0.353703415234045,0.341173431307316,0.345578512726934,0.358159779825909,
0.334687181997538,0.337442516960342,0.343721563062338,0.336509253287721,0.325271170690837,
0.325488235114597,0.32078065970396,0.317594707821212,0.314613974963111,0.309774332543378,
0.307619999017408,0.307004105181405,0.300279349768979,0.305505356875903,0.303179706053309,
0.312783673753436,0.308540965611869,0.292690196360757,0.299428992380521,0.297144304197462,
0.286701832971995,0.297894654636997,0.283984127549023,0.283253709389766,0.281330372503553,
0.289052362087009,0.272730959781483,0.277399161038311,0.285764741944136,0.271195118636169)
)
test_that("Zalpha_rsq_over_expected fails when LDprofile_bins are not of equal size", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = tempLDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"LDprofile_bins must be of equal size")
})
## Test the function with LDprofile_rsq non-numeric
test_that("Zalpha_rsq_over_expected fails when LDprofile_rsq is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = paste0(LDprofile$rsq,"r"), minRandL = 4, minRL = 25, X = NULL),
"LDprofile_rsq must be a numeric vector")
})
## Test the function with LDprofile_rsq having values outside (0,1)
tempLDprofile<-data.frame(
bin=seq(0,0.0049,0.0001),
rsq=c(3,0.411014233619574,0.395532914859378,0.44354526861954,0.435550945945946,
0.419534577303153,0.383410708498866,0.402439897670834,0.395945237932081,0.380436909495495,
0.384229510773621,0.379494011054621,0.368118044626627,0.358753523652643,0.362330915047976,
0.372142680938693,0.353703415234045,0.341173431307316,0.345578512726934,0.358159779825909,
0.334687181997538,0.337442516960342,0.343721563062338,0.336509253287721,0.325271170690837,
0.325488235114597,0.32078065970396,0.317594707821212,0.314613974963111,0.309774332543378,
0.307619999017408,0.307004105181405,0.300279349768979,0.305505356875903,0.303179706053309,
0.312783673753436,0.308540965611869,0.292690196360757,0.299428992380521,0.297144304197462,
0.286701832971995,0.297894654636997,0.283984127549023,0.283253709389766,0.281330372503553,
0.289052362087009,0.272730959781483,0.277399161038311,0.285764741944136,0.271195118636169)
)
test_that("Zalpha_rsq_over_expected fails when LDprofile_rsq contains values not between 0 and 1", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = tempLDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"Values stored in LDprofile_rsq must be between 0 and 1")
})
## Test the function with x not a matrix
test_that("Zalpha_rsq_over_expected fails when x is not a matrix", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = df[,3:7], dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails when the number of rows in x is not equal to the length of pos", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = t(as.matrix(df[,3:7])), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, 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("Zalpha_rsq_over_expected fails when a SNP has only one allele", {
df1<-df
df1[1,3:7]<-1
expect_error(Zalpha_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"SNPs must all be biallelic")
})
## Test the function with a SNP having more than two alleles
test_that("Zalpha_rsq_over_expected fails when a SNP has more than two alleles", {
df1<-df
df1[1,7]<-3
expect_error(Zalpha_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"SNPs must all be biallelic")
})
## Test the function with LDprofile_bins is a different length to LDprofile_rsq
test_that("Zalpha_rsq_over_expected fails when LDprofile_bins and LDprofile_rsq are different lengths", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$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 that Zalpha_rsq_over_expected works with a missing value
df1<-df
df1$C1[15]<-NA
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with missing value", {
expect_equal(Zalpha_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df1$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
Zalpha_rsq_over_expected=c(NA,NA,NA,NA,
1.144893254873100,
1.236446352382830,
1.020556368226920,
0.810519367025429,
0.761404523358315,
0.823237169574888,
0.907695973532459,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## test what happens when the biggest bin is bigger than the max_dist in the LDprofile
df1<-df
df1$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)
})
Try the zalpha package in your browser
Any scripts or data that you put into this service are public.
zalpha documentation built on Nov. 27, 2021, 9:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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),
dist=c(0,0.00101,0.00123,0.00207,0.00218,0.00223,0.00235,0.00251,0.00272,0.00289,0.00304,0.00316,0.00335,0.00345,0.00374)
)
LDprofile<-data.frame(
bin=seq(0,0.0049,0.0001),
rsq=c(0.495714059385946,0.411014233619574,0.395532914859378,0.44354526861954,0.435550945945946,
0.419534577303153,0.383410708498866,0.402439897670834,0.395945237932081,0.380436909495495,
0.384229510773621,0.379494011054621,0.368118044626627,0.358753523652643,0.362330915047976,
0.372142680938693,0.353703415234045,0.341173431307316,0.345578512726934,0.358159779825909,
0.334687181997538,0.337442516960342,0.343721563062338,0.336509253287721,0.325271170690837,
0.325488235114597,0.32078065970396,0.317594707821212,0.314613974963111,0.309774332543378,
0.307619999017408,0.307004105181405,0.300279349768979,0.305505356875903,0.303179706053309,
0.312783673753436,0.308540965611869,0.292690196360757,0.299428992380521,0.297144304197462,
0.286701832971995,0.297894654636997,0.283984127549023,0.283253709389766,0.281330372503553,
0.289052362087009,0.272730959781483,0.277399161038311,0.285764741944136,0.271195118636169)
)
## test that Zalpha_rsq_over_expected is calculated correctly
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly", {
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
Zalpha_rsq_over_expected=c(NA,NA,NA,NA,
1.099392777415350,
1.175423932431810,
0.973208670564282,
0.767152145198758,
0.691051112331195,
0.728230393808371,
0.737847444047460,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with a different window size
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with a different window size", {
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 1100, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
Zalpha_rsq_over_expected=c(NA,NA,NA,NA,NA,
1.120554321638970,
0.961086582792753,
0.658704548108426,
0.499640647493653,
0.478776705516631,
NA,NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with a character matrix as x
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with character matrix", {
df1<-df
df1[df1==1]<-"A"
df1[df1==2]<-"B"
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
list(
position=c(100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500),
Zalpha_rsq_over_expected=c(NA,NA,NA,NA,
1.099392777415350,
1.175423932431810,
0.973208670564282,
0.767152145198758,
0.691051112331195,
0.728230393808371,
0.737847444047460,
NA,NA,NA,NA)
),tolerance=0.0001)
})
## Test the function with X supplied as a parameter
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with X supplied", {
expect_equal(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = c(700,900)),
list(
position=c(700,800,900),
Zalpha_rsq_over_expected=c(0.973208670564282,
0.767152145198758,
0.691051112331195)
),tolerance=0.0001)
})
## Test the function with X supplied as a parameter outside of the region defined in pos
test_that("Zalpha_rsq_over_expected fails with an X supplied outside of the region defined in pos", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = c(7000,9000)),
"The region specified by X is outside the region contained in the pos vector")
})
## Test the function with X supplied as character
test_that("Zalpha_rsq_over_expected fails with an X supplied as a character", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = c("700bp","900bp")),
"X should be a numeric vector of length 2 e.g. c(100,200)",
fixed=TRUE)
})
## Test the function with X supplied as only one number
test_that("Zalpha_rsq_over_expected fails with an X supplied as only one number", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = 700),
"X should be a numeric vector of length 2 e.g. c(100,200)",
fixed=TRUE)
})
## Test the function with X supplied with too many numbers
test_that("Zalpha_rsq_over_expected fails with an X supplied with too many numbers", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = c(700,900,1100)),
"X should be a numeric vector of length 2 e.g. c(100,200)",
fixed=TRUE)
})
## Test the function with ws non-numeric
test_that("Zalpha_rsq_over_expected fails when ws is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = "3000bp", x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"ws must be a number greater than 0")
})
## Test the function with ws = 0
test_that("Zalpha_rsq_over_expected fails when ws is zero", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 0, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"ws must be a number greater than 0")
})
## Test the function with positions non-numeric
test_that("Zalpha_rsq_over_expected fails when pos is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = paste0(df$POS,"bp"), ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"pos must be a numeric vector")
})
## Test the function with minLandR as non-numeric
test_that("Zalpha_rsq_over_expected fails when minLandR is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = "4snps", minRL = 25, X = NULL),
"minRandL must be a number greater than or equal to 0")
})
## Test the function with minLandR as negative
test_that("Zalpha_rsq_over_expected fails when minLandR is negative", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = -1, minRL = 25, X = NULL),
"minRandL must be a number greater than or equal to 0")
})
## Test the function with minLR as non-numeric
test_that("Zalpha_rsq_over_expected fails when minLR is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = "25b", X = NULL),
"minRL must be a number greater than or equal to 0")
})
## Test the function with minLR as negative
test_that("Zalpha_rsq_over_expected fails when minLR is negative", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = -25, X = NULL),
"minRL must be a number greater than or equal to 0")
})
## Test the warning that all values returned are NA by increasing minRL
test_that("Zalpha_rsq_over_expected warns about all NAs", {
expect_warning(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 50, X = NULL),
"No Zalpha_rsq_over_expected values were calculated, try reducing minRandL and minRL or increasing the window size")
})
## Test the function with dists non-numeric
test_that("Zalpha_rsq_over_expected fails when dist is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = paste0(df$dist,"dist"), LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"dist must be a numeric vector")
})
## Test the function with dists a different length to pos
test_that("Zalpha_rsq_over_expected fails when dist is a different length to pos", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = c(df$dist,1), LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"The number of values in dist must equal the number of SNP locations given in pos")
})
## Test the function with LDprofile_bins non-numeric
test_that("Zalpha_rsq_over_expected fails when LDprofile_bins is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = paste0(LDprofile$bin,"dist"), LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"LDprofile_bins must be a numeric vector")
})
## Test the function with LDprofile_bins not of equal size
tempLDprofile<-data.frame(
bin=c(seq(0,0.0048,0.0001),3),
rsq=c(0.495714059385946,0.411014233619574,0.395532914859378,0.44354526861954,0.435550945945946,
0.419534577303153,0.383410708498866,0.402439897670834,0.395945237932081,0.380436909495495,
0.384229510773621,0.379494011054621,0.368118044626627,0.358753523652643,0.362330915047976,
0.372142680938693,0.353703415234045,0.341173431307316,0.345578512726934,0.358159779825909,
0.334687181997538,0.337442516960342,0.343721563062338,0.336509253287721,0.325271170690837,
0.325488235114597,0.32078065970396,0.317594707821212,0.314613974963111,0.309774332543378,
0.307619999017408,0.307004105181405,0.300279349768979,0.305505356875903,0.303179706053309,
0.312783673753436,0.308540965611869,0.292690196360757,0.299428992380521,0.297144304197462,
0.286701832971995,0.297894654636997,0.283984127549023,0.283253709389766,0.281330372503553,
0.289052362087009,0.272730959781483,0.277399161038311,0.285764741944136,0.271195118636169)
)
test_that("Zalpha_rsq_over_expected fails when LDprofile_bins are not of equal size", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = tempLDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"LDprofile_bins must be of equal size")
})
## Test the function with LDprofile_rsq non-numeric
test_that("Zalpha_rsq_over_expected fails when LDprofile_rsq is non-numeric", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = paste0(LDprofile$rsq,"r"), minRandL = 4, minRL = 25, X = NULL),
"LDprofile_rsq must be a numeric vector")
})
## Test the function with LDprofile_rsq having values outside (0,1)
tempLDprofile<-data.frame(
bin=seq(0,0.0049,0.0001),
rsq=c(3,0.411014233619574,0.395532914859378,0.44354526861954,0.435550945945946,
0.419534577303153,0.383410708498866,0.402439897670834,0.395945237932081,0.380436909495495,
0.384229510773621,0.379494011054621,0.368118044626627,0.358753523652643,0.362330915047976,
0.372142680938693,0.353703415234045,0.341173431307316,0.345578512726934,0.358159779825909,
0.334687181997538,0.337442516960342,0.343721563062338,0.336509253287721,0.325271170690837,
0.325488235114597,0.32078065970396,0.317594707821212,0.314613974963111,0.309774332543378,
0.307619999017408,0.307004105181405,0.300279349768979,0.305505356875903,0.303179706053309,
0.312783673753436,0.308540965611869,0.292690196360757,0.299428992380521,0.297144304197462,
0.286701832971995,0.297894654636997,0.283984127549023,0.283253709389766,0.281330372503553,
0.289052362087009,0.272730959781483,0.277399161038311,0.285764741944136,0.271195118636169)
)
test_that("Zalpha_rsq_over_expected fails when LDprofile_rsq contains values not between 0 and 1", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = tempLDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"Values stored in LDprofile_rsq must be between 0 and 1")
})
## Test the function with x not a matrix
test_that("Zalpha_rsq_over_expected fails when x is not a matrix", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = df[,3:7], dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"x must be a matrix")
})
## Test the function with x not having the correct amount of rows
test_that("Zalpha_rsq_over_expected fails when the number of rows in x is not equal to the length of pos", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = t(as.matrix(df[,3:7])), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"The number of rows in x must equal the number of SNP locations given in pos")
})
## Test the function with a SNP having only one allele
test_that("Zalpha_rsq_over_expected fails when a SNP has only one allele", {
df1<-df
df1[1,3:7]<-1
expect_error(Zalpha_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"SNPs must all be biallelic")
})
## Test the function with a SNP having more than two alleles
test_that("Zalpha_rsq_over_expected fails when a SNP has more than two alleles", {
df1<-df
df1[1,7]<-3
expect_error(Zalpha_rsq_over_expected(pos = df1$POS, ws = 3000, x = as.matrix(df1[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = LDprofile$rsq, minRandL = 4, minRL = 25, X = NULL),
"SNPs must all be biallelic")
})
## Test the function with LDprofile_bins is a different length to LDprofile_rsq
test_that("Zalpha_rsq_over_expected fails when LDprofile_bins and LDprofile_rsq are different lengths", {
expect_error(Zalpha_rsq_over_expected(pos = df$POS, ws = 3000, x = as.matrix(df[,3:7]), dist = df$dist, LDprofile_bins = LDprofile$bin, LDprofile_rsq = c(LDprofile$rsq,1), minRandL = 4, minRL = 25, X = NULL),
"LDprofile_rsq must contain the same number of values as there are bins given in LDprofile_bins")
})
## test that Zalpha_rsq_over_expected works with a missing value
df1<-df
df1$C1[15]<-NA
test_that("Zalpha_rsq_over_expected calculates Zalpha_rsq_over_expected statistic correctly with missing value", {
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,
1.144893254873100,
1.236446352382830,
1.020556368226920,
0.810519367025429,
0.761404523358315,
0.823237169574888,
0.907695973532459,
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)
})
Try the zalpha package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.