tests/testthat/test-calculateHb.r
In OskarHansson/strvalidator: Process Control and Validation of Forensic STR Kits
context("calculateHb")
################################################################################
# CHANGE LOG
# 22.03.2019: Changed deprecated 'matches' to 'expect_match'.
# 29.08.2016: First tests 1-11.
#
# require(strvalidator)
# require(testthat)
# test_dir("inst/tests/")
# test_file("tests/testthat/test-calculateHb.r")
# test_dir("tests/testthat")
test_that("calculateHb", {
# Get SGM Plus test data.
data("set2")
data("ref2")
# Get Fusion test data and extract one sample.
data("set6")
set6 <- subset(set6, Sample.Name == "D_0.50000NG-2")
data("ref61")
data("ref62")
# Create a dataset with two equally high maximum peaks.
setEqual <- set2
setEqual[setEqual$Marker == "D3S1358", ]$Height <- 400
setEqual[setEqual$Marker == "D18S51", ]$Height <- 550
# Create a dataset with extra peaks (unfiltered data).
setUnfiltered <- set2
extraName <- c("SampleA01", "SampleA01", "SampleA02")
extraMarker <- c("D3S1358", "D16S539", "FGA")
extraAllele <- c("17", "10", "24")
extraHeight <- c(50, 400, 40)
extraDye <- c("B", "B", "Y")
extra <- data.frame(
Sample.Name = extraName,
Marker = extraMarker,
Allele = extraAllele,
Height = extraHeight,
Dye = extraDye,
stringsAsFactors = FALSE
)
setUnfiltered <- rbind(setUnfiltered, extra)
# TEST 01 -------------------------------------------------------------------
# Test normal calculation of hb=1.
# Analyse dataframe.
res <- calculateHb(data = set2, ref = ref2, hb = 1, kit = "SGMplus", ignore.case = TRUE)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_false(is.null(res$Sample.Name))
expect_false(is.null(res$Marker))
expect_false(is.null(res$Dye))
expect_false(is.null(res$Delta))
expect_false(is.null(res$HMW))
expect_false(is.null(res$LMW))
expect_false(is.null(res$MPH))
expect_false(is.null(res$Hb))
# Check for NA's.
expect_false(any(is.na(res$Sample.Name)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Dye)))
expect_false(any(is.na(res$Delta)))
expect_false(any(is.na(res$HMW)))
expect_false(any(is.na(res$LMW)))
expect_false(any(is.na(res$MPH)))
expect_false(any(is.na(res$Hb)))
# Check result: Repeat unit difference.
expect_that(res$Delta[1], equals(3))
expect_that(res$Delta[2], equals(2))
expect_that(res$Delta[3], equals(1))
expect_that(res$Delta[4], equals(15.2))
expect_that(res$Delta[5], equals(4))
expect_that(res$Delta[6], equals(3))
expect_that(res$Delta[7], equals(2))
expect_that(res$Delta[8], equals(1))
expect_that(res$Delta[9], equals(15.2))
expect_that(res$Delta[10], equals(4))
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(491 / 423))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(384 / 359))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(241 / 198))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(431))
expect_that(res$MPH[2], equals(457))
expect_that(res$MPH[3], equals(609.5))
expect_that(res$MPH[4], equals(379.5))
expect_that(res$MPH[5], equals(371.5))
expect_that(res$MPH[6], equals(220))
expect_that(res$MPH[7], equals(219.5))
expect_that(res$MPH[8], equals(319))
expect_that(res$MPH[9], equals(200.5))
expect_that(res$MPH[10], equals(181))
# TEST 02 -------------------------------------------------------------------
# Test normal calculation of hb=2.
# Analyse dataframe.
res <- calculateHb(data = set2, ref = ref2, hb = 2, kit = "SGMplus", ignore.case = TRUE)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_false(is.null(res$Sample.Name))
expect_false(is.null(res$Marker))
expect_false(is.null(res$Dye))
expect_false(is.null(res$Delta))
expect_false(is.null(res$LMW))
expect_false(is.null(res$HMW))
expect_false(is.null(res$MPH))
expect_false(is.null(res$Hb))
# Check for NA's.
expect_false(any(is.na(res$Sample.Name)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Dye)))
expect_false(any(is.na(res$Delta)))
expect_false(any(is.na(res$LMW)))
expect_false(any(is.na(res$HMW)))
expect_false(any(is.na(res$MPH)))
expect_false(any(is.na(res$Hb)))
# Check result: Repeat unit difference.
expect_that(res$Delta[1], equals(3))
expect_that(res$Delta[2], equals(2))
expect_that(res$Delta[3], equals(1))
expect_that(res$Delta[4], equals(15.2))
expect_that(res$Delta[5], equals(4))
expect_that(res$Delta[6], equals(3))
expect_that(res$Delta[7], equals(2))
expect_that(res$Delta[8], equals(1))
expect_that(res$Delta[9], equals(15.2))
expect_that(res$Delta[10], equals(4))
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(460 / 402))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(632 / 587))
expect_that(res$Hb[4], equals(398 / 361))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(225 / 215))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(326 / 312))
expect_that(res$Hb[9], equals(206 / 195))
expect_that(res$Hb[10], equals(183 / 179))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(431))
expect_that(res$MPH[2], equals(457))
expect_that(res$MPH[3], equals(609.5))
expect_that(res$MPH[4], equals(379.5))
expect_that(res$MPH[5], equals(371.5))
expect_that(res$MPH[6], equals(220))
expect_that(res$MPH[7], equals(219.5))
expect_that(res$MPH[8], equals(319))
expect_that(res$MPH[9], equals(200.5))
expect_that(res$MPH[10], equals(181))
# TEST 03 -------------------------------------------------------------------
# Test normal calculation of hb=3.
# Analyse dataframe.
res <- calculateHb(data = set2, ref = ref2, hb = 3, kit = "SGMplus", ignore.case = TRUE)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_false(is.null(res$Sample.Name))
expect_false(is.null(res$Marker))
expect_false(is.null(res$Dye))
expect_false(is.null(res$Delta))
expect_false(is.null(res$Small))
expect_false(is.null(res$Large))
expect_false(is.null(res$MPH))
expect_false(is.null(res$Hb))
# Check for NA's.
expect_false(any(is.na(res$Sample.Name)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Dye)))
expect_false(any(is.na(res$Delta)))
expect_false(any(is.na(res$Small)))
expect_false(any(is.na(res$Large)))
expect_false(any(is.na(res$MPH)))
expect_false(any(is.na(res$Hb)))
# Check result: Repeat unit difference.
expect_that(res$Delta[1], equals(3))
expect_that(res$Delta[2], equals(2))
expect_that(res$Delta[3], equals(1))
expect_that(res$Delta[4], equals(15.2))
expect_that(res$Delta[5], equals(4))
expect_that(res$Delta[6], equals(3))
expect_that(res$Delta[7], equals(2))
expect_that(res$Delta[8], equals(1))
expect_that(res$Delta[9], equals(15.2))
expect_that(res$Delta[10], equals(4))
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(431))
expect_that(res$MPH[2], equals(457))
expect_that(res$MPH[3], equals(609.5))
expect_that(res$MPH[4], equals(379.5))
expect_that(res$MPH[5], equals(371.5))
expect_that(res$MPH[6], equals(220))
expect_that(res$MPH[7], equals(219.5))
expect_that(res$MPH[8], equals(319))
expect_that(res$MPH[9], equals(200.5))
expect_that(res$MPH[10], equals(181))
# TEST 04 -------------------------------------------------------------------
# Test that two equally high maximum peaks works.
# Analyse dataframe.
res <- calculateHb(
data = setEqual, ref = ref2, hb = 1,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(1))
expect_that(res$Hb[2], equals(491 / 423))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(1))
expect_that(res$Hb[5], equals(384 / 359))
expect_that(res$Hb[6], equals(1))
expect_that(res$Hb[7], equals(241 / 198))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(1))
expect_that(res$Hb[10], equals(179 / 183))
# Analyse dataframe.
res <- calculateHb(
data = setEqual, ref = ref2, hb = 2,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(1))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(632 / 587))
expect_that(res$Hb[4], equals(1))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(1))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(326 / 312))
expect_that(res$Hb[9], equals(1))
expect_that(res$Hb[10], equals(183 / 179))
# Analyse dataframe.
res <- calculateHb(
data = setEqual, ref = ref2, hb = 3,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(1))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(1))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(1))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(1))
expect_that(res$Hb[10], equals(179 / 183))
# TEST 05 -------------------------------------------------------------------
# Test that unfiltered data works.
# Analyse dataframe.
res <- calculateHb(
data = setUnfiltered, ref = ref2, hb = 1,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(491 / 423))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(384 / 359))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(241 / 198))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# Analyse dataframe.
res <- calculateHb(
data = setUnfiltered, ref = ref2, hb = 2,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(460 / 402))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(632 / 587))
expect_that(res$Hb[4], equals(398 / 361))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(225 / 215))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(326 / 312))
expect_that(res$Hb[9], equals(206 / 195))
expect_that(res$Hb[10], equals(183 / 179))
# Analyse dataframe.
res <- calculateHb(
data = setUnfiltered, ref = ref2, hb = 3,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# TEST 06 -------------------------------------------------------------------
# Test that different marker order in ref and data works for hb=1.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref61, hb = 1, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(10166 / 7985))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(9975 / 7715))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(6329 / 5730))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15485 / 15388))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(7703 / 6465))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(5063 / 4745))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(12385 / 7159))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 07 -------------------------------------------------------------------
# Test that different marker order in ref and data works for hb=2.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref61, hb = 2, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(10860 / 9708))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5835 / 5653))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(6831 / 3829))
expect_that(res$Hb[7], equals(23147 / 21648))
expect_that(res$Hb[8], equals(13931 / 10570))
expect_that(res$Hb[9], equals(10028 / 7275))
expect_that(res$Hb[10], equals(4312 / 3774))
expect_that(res$Hb[11], equals(4196 / 2772))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(8630 / 6422))
expect_that(res$Hb[14], equals(8860 / 8769))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5203 / 5132))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(13568 / 10837))
expect_that(res$Hb[19], equals(16027 / 11850))
expect_that(res$Hb[20], equals(11523 / 8669))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3471 / 3341))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 08 -------------------------------------------------------------------
# Test that different marker order in ref and data works for hb=3.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref61, hb = 3, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 09 -------------------------------------------------------------------
# Test that identical marker order in ref and data works for hb=1.
res <- calculateHb(data = set6, ref = ref62, hb = 1, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(10166 / 7985))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(9975 / 7715))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(6329 / 5730))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15485 / 15388))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(7703 / 6465))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(5063 / 4745))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(12385 / 7159))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 10 -------------------------------------------------------------------
# Test that identical marker order in ref and data works for hb=2.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref62, hb = 2, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(10860 / 9708))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5835 / 5653))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(6831 / 3829))
expect_that(res$Hb[7], equals(23147 / 21648))
expect_that(res$Hb[8], equals(13931 / 10570))
expect_that(res$Hb[9], equals(10028 / 7275))
expect_that(res$Hb[10], equals(4312 / 3774))
expect_that(res$Hb[11], equals(4196 / 2772))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(8630 / 6422))
expect_that(res$Hb[14], equals(8860 / 8769))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5203 / 5132))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(13568 / 10837))
expect_that(res$Hb[19], equals(16027 / 11850))
expect_that(res$Hb[20], equals(11523 / 8669))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3471 / 3341))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 11 -------------------------------------------------------------------
# Test that identical marker order in ref and data works for hb=3.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref62, hb = 3, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
})
OskarHansson/strvalidator documentation built on July 22, 2023, 12:04 p.m.
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context("calculateHb")
################################################################################
# CHANGE LOG
# 22.03.2019: Changed deprecated 'matches' to 'expect_match'.
# 29.08.2016: First tests 1-11.
#
# require(strvalidator)
# require(testthat)
# test_dir("inst/tests/")
# test_file("tests/testthat/test-calculateHb.r")
# test_dir("tests/testthat")
test_that("calculateHb", {
# Get SGM Plus test data.
data("set2")
data("ref2")
# Get Fusion test data and extract one sample.
data("set6")
set6 <- subset(set6, Sample.Name == "D_0.50000NG-2")
data("ref61")
data("ref62")
# Create a dataset with two equally high maximum peaks.
setEqual <- set2
setEqual[setEqual$Marker == "D3S1358", ]$Height <- 400
setEqual[setEqual$Marker == "D18S51", ]$Height <- 550
# Create a dataset with extra peaks (unfiltered data).
setUnfiltered <- set2
extraName <- c("SampleA01", "SampleA01", "SampleA02")
extraMarker <- c("D3S1358", "D16S539", "FGA")
extraAllele <- c("17", "10", "24")
extraHeight <- c(50, 400, 40)
extraDye <- c("B", "B", "Y")
extra <- data.frame(
Sample.Name = extraName,
Marker = extraMarker,
Allele = extraAllele,
Height = extraHeight,
Dye = extraDye,
stringsAsFactors = FALSE
)
setUnfiltered <- rbind(setUnfiltered, extra)
# TEST 01 -------------------------------------------------------------------
# Test normal calculation of hb=1.
# Analyse dataframe.
res <- calculateHb(data = set2, ref = ref2, hb = 1, kit = "SGMplus", ignore.case = TRUE)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_false(is.null(res$Sample.Name))
expect_false(is.null(res$Marker))
expect_false(is.null(res$Dye))
expect_false(is.null(res$Delta))
expect_false(is.null(res$HMW))
expect_false(is.null(res$LMW))
expect_false(is.null(res$MPH))
expect_false(is.null(res$Hb))
# Check for NA's.
expect_false(any(is.na(res$Sample.Name)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Dye)))
expect_false(any(is.na(res$Delta)))
expect_false(any(is.na(res$HMW)))
expect_false(any(is.na(res$LMW)))
expect_false(any(is.na(res$MPH)))
expect_false(any(is.na(res$Hb)))
# Check result: Repeat unit difference.
expect_that(res$Delta[1], equals(3))
expect_that(res$Delta[2], equals(2))
expect_that(res$Delta[3], equals(1))
expect_that(res$Delta[4], equals(15.2))
expect_that(res$Delta[5], equals(4))
expect_that(res$Delta[6], equals(3))
expect_that(res$Delta[7], equals(2))
expect_that(res$Delta[8], equals(1))
expect_that(res$Delta[9], equals(15.2))
expect_that(res$Delta[10], equals(4))
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(491 / 423))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(384 / 359))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(241 / 198))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(431))
expect_that(res$MPH[2], equals(457))
expect_that(res$MPH[3], equals(609.5))
expect_that(res$MPH[4], equals(379.5))
expect_that(res$MPH[5], equals(371.5))
expect_that(res$MPH[6], equals(220))
expect_that(res$MPH[7], equals(219.5))
expect_that(res$MPH[8], equals(319))
expect_that(res$MPH[9], equals(200.5))
expect_that(res$MPH[10], equals(181))
# TEST 02 -------------------------------------------------------------------
# Test normal calculation of hb=2.
# Analyse dataframe.
res <- calculateHb(data = set2, ref = ref2, hb = 2, kit = "SGMplus", ignore.case = TRUE)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_false(is.null(res$Sample.Name))
expect_false(is.null(res$Marker))
expect_false(is.null(res$Dye))
expect_false(is.null(res$Delta))
expect_false(is.null(res$LMW))
expect_false(is.null(res$HMW))
expect_false(is.null(res$MPH))
expect_false(is.null(res$Hb))
# Check for NA's.
expect_false(any(is.na(res$Sample.Name)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Dye)))
expect_false(any(is.na(res$Delta)))
expect_false(any(is.na(res$LMW)))
expect_false(any(is.na(res$HMW)))
expect_false(any(is.na(res$MPH)))
expect_false(any(is.na(res$Hb)))
# Check result: Repeat unit difference.
expect_that(res$Delta[1], equals(3))
expect_that(res$Delta[2], equals(2))
expect_that(res$Delta[3], equals(1))
expect_that(res$Delta[4], equals(15.2))
expect_that(res$Delta[5], equals(4))
expect_that(res$Delta[6], equals(3))
expect_that(res$Delta[7], equals(2))
expect_that(res$Delta[8], equals(1))
expect_that(res$Delta[9], equals(15.2))
expect_that(res$Delta[10], equals(4))
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(460 / 402))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(632 / 587))
expect_that(res$Hb[4], equals(398 / 361))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(225 / 215))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(326 / 312))
expect_that(res$Hb[9], equals(206 / 195))
expect_that(res$Hb[10], equals(183 / 179))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(431))
expect_that(res$MPH[2], equals(457))
expect_that(res$MPH[3], equals(609.5))
expect_that(res$MPH[4], equals(379.5))
expect_that(res$MPH[5], equals(371.5))
expect_that(res$MPH[6], equals(220))
expect_that(res$MPH[7], equals(219.5))
expect_that(res$MPH[8], equals(319))
expect_that(res$MPH[9], equals(200.5))
expect_that(res$MPH[10], equals(181))
# TEST 03 -------------------------------------------------------------------
# Test normal calculation of hb=3.
# Analyse dataframe.
res <- calculateHb(data = set2, ref = ref2, hb = 3, kit = "SGMplus", ignore.case = TRUE)
# Check return class.
expect_match(class(res), class(data.frame()))
# Check that expected columns exist.
expect_false(is.null(res$Sample.Name))
expect_false(is.null(res$Marker))
expect_false(is.null(res$Dye))
expect_false(is.null(res$Delta))
expect_false(is.null(res$Small))
expect_false(is.null(res$Large))
expect_false(is.null(res$MPH))
expect_false(is.null(res$Hb))
# Check for NA's.
expect_false(any(is.na(res$Sample.Name)))
expect_false(any(is.na(res$Marker)))
expect_false(any(is.na(res$Dye)))
expect_false(any(is.na(res$Delta)))
expect_false(any(is.na(res$Small)))
expect_false(any(is.na(res$Large)))
expect_false(any(is.na(res$MPH)))
expect_false(any(is.na(res$Hb)))
# Check result: Repeat unit difference.
expect_that(res$Delta[1], equals(3))
expect_that(res$Delta[2], equals(2))
expect_that(res$Delta[3], equals(1))
expect_that(res$Delta[4], equals(15.2))
expect_that(res$Delta[5], equals(4))
expect_that(res$Delta[6], equals(3))
expect_that(res$Delta[7], equals(2))
expect_that(res$Delta[8], equals(1))
expect_that(res$Delta[9], equals(15.2))
expect_that(res$Delta[10], equals(4))
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(431))
expect_that(res$MPH[2], equals(457))
expect_that(res$MPH[3], equals(609.5))
expect_that(res$MPH[4], equals(379.5))
expect_that(res$MPH[5], equals(371.5))
expect_that(res$MPH[6], equals(220))
expect_that(res$MPH[7], equals(219.5))
expect_that(res$MPH[8], equals(319))
expect_that(res$MPH[9], equals(200.5))
expect_that(res$MPH[10], equals(181))
# TEST 04 -------------------------------------------------------------------
# Test that two equally high maximum peaks works.
# Analyse dataframe.
res <- calculateHb(
data = setEqual, ref = ref2, hb = 1,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(1))
expect_that(res$Hb[2], equals(491 / 423))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(1))
expect_that(res$Hb[5], equals(384 / 359))
expect_that(res$Hb[6], equals(1))
expect_that(res$Hb[7], equals(241 / 198))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(1))
expect_that(res$Hb[10], equals(179 / 183))
# Analyse dataframe.
res <- calculateHb(
data = setEqual, ref = ref2, hb = 2,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(1))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(632 / 587))
expect_that(res$Hb[4], equals(1))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(1))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(326 / 312))
expect_that(res$Hb[9], equals(1))
expect_that(res$Hb[10], equals(183 / 179))
# Analyse dataframe.
res <- calculateHb(
data = setEqual, ref = ref2, hb = 3,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(1))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(1))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(1))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(1))
expect_that(res$Hb[10], equals(179 / 183))
# TEST 05 -------------------------------------------------------------------
# Test that unfiltered data works.
# Analyse dataframe.
res <- calculateHb(
data = setUnfiltered, ref = ref2, hb = 1,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(491 / 423))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(384 / 359))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(241 / 198))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# Analyse dataframe.
res <- calculateHb(
data = setUnfiltered, ref = ref2, hb = 2,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(460 / 402))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(632 / 587))
expect_that(res$Hb[4], equals(398 / 361))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(225 / 215))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(326 / 312))
expect_that(res$Hb[9], equals(206 / 195))
expect_that(res$Hb[10], equals(183 / 179))
# Analyse dataframe.
res <- calculateHb(
data = setUnfiltered, ref = ref2, hb = 3,
kit = "SGMplus", ignore.case = TRUE
)
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(402 / 460))
expect_that(res$Hb[2], equals(423 / 491))
expect_that(res$Hb[3], equals(587 / 632))
expect_that(res$Hb[4], equals(361 / 398))
expect_that(res$Hb[5], equals(359 / 384))
expect_that(res$Hb[6], equals(215 / 225))
expect_that(res$Hb[7], equals(198 / 241))
expect_that(res$Hb[8], equals(312 / 326))
expect_that(res$Hb[9], equals(195 / 206))
expect_that(res$Hb[10], equals(179 / 183))
# TEST 06 -------------------------------------------------------------------
# Test that different marker order in ref and data works for hb=1.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref61, hb = 1, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(10166 / 7985))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(9975 / 7715))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(6329 / 5730))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15485 / 15388))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(7703 / 6465))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(5063 / 4745))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(12385 / 7159))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 07 -------------------------------------------------------------------
# Test that different marker order in ref and data works for hb=2.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref61, hb = 2, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(10860 / 9708))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5835 / 5653))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(6831 / 3829))
expect_that(res$Hb[7], equals(23147 / 21648))
expect_that(res$Hb[8], equals(13931 / 10570))
expect_that(res$Hb[9], equals(10028 / 7275))
expect_that(res$Hb[10], equals(4312 / 3774))
expect_that(res$Hb[11], equals(4196 / 2772))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(8630 / 6422))
expect_that(res$Hb[14], equals(8860 / 8769))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5203 / 5132))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(13568 / 10837))
expect_that(res$Hb[19], equals(16027 / 11850))
expect_that(res$Hb[20], equals(11523 / 8669))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3471 / 3341))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 08 -------------------------------------------------------------------
# Test that different marker order in ref and data works for hb=3.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref61, hb = 3, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 09 -------------------------------------------------------------------
# Test that identical marker order in ref and data works for hb=1.
res <- calculateHb(data = set6, ref = ref62, hb = 1, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(10166 / 7985))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(9975 / 7715))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(6329 / 5730))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15485 / 15388))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(7703 / 6465))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(5063 / 4745))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(12385 / 7159))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 10 -------------------------------------------------------------------
# Test that identical marker order in ref and data works for hb=2.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref62, hb = 2, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(10860 / 9708))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5835 / 5653))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(6831 / 3829))
expect_that(res$Hb[7], equals(23147 / 21648))
expect_that(res$Hb[8], equals(13931 / 10570))
expect_that(res$Hb[9], equals(10028 / 7275))
expect_that(res$Hb[10], equals(4312 / 3774))
expect_that(res$Hb[11], equals(4196 / 2772))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(8630 / 6422))
expect_that(res$Hb[14], equals(8860 / 8769))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5203 / 5132))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(13568 / 10837))
expect_that(res$Hb[19], equals(16027 / 11850))
expect_that(res$Hb[20], equals(11523 / 8669))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3471 / 3341))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
# TEST 11 -------------------------------------------------------------------
# Test that identical marker order in ref and data works for hb=3.
# Analyse dataframe.
res <- calculateHb(data = set6, ref = ref62, hb = 3, kit = "Fusion")
# Check result: Heterozygous balance.
expect_that(res$Hb[1], equals(7985 / 10166))
expect_that(res$Hb[2], equals(9708 / 10860))
expect_that(res$Hb[3], equals(7715 / 9975))
expect_that(res$Hb[4], equals(5653 / 5835))
expect_that(res$Hb[5], equals(5730 / 6329))
expect_that(res$Hb[6], equals(3829 / 6831))
expect_that(res$Hb[7], equals(21648 / 23147))
expect_that(res$Hb[8], equals(10570 / 13931))
expect_that(res$Hb[9], equals(7275 / 10028))
expect_that(res$Hb[10], equals(3774 / 4312))
expect_that(res$Hb[11], equals(2772 / 4196))
expect_that(res$Hb[12], equals(15388 / 15485))
expect_that(res$Hb[13], equals(6422 / 8630))
expect_that(res$Hb[14], equals(8769 / 8860))
expect_that(res$Hb[15], equals(6465 / 7703))
expect_that(res$Hb[16], equals(5132 / 5203))
expect_that(res$Hb[17], equals(4745 / 5063))
expect_that(res$Hb[18], equals(10837 / 13568))
expect_that(res$Hb[19], equals(11850 / 16027))
expect_that(res$Hb[20], equals(8669 / 11523))
expect_that(res$Hb[21], equals(7159 / 12385))
expect_that(res$Hb[22], equals(3341 / 3471))
# Check result: Mean peak height.
expect_that(res$MPH[1], equals(9075.5))
expect_that(res$MPH[2], equals(10284))
expect_that(res$MPH[3], equals(8845))
expect_that(res$MPH[4], equals(5744))
expect_that(res$MPH[5], equals(6029.5))
expect_that(res$MPH[6], equals(5330))
expect_that(res$MPH[7], equals(22397.5))
expect_that(res$MPH[8], equals(12250.5))
expect_that(res$MPH[9], equals(8651.5))
expect_that(res$MPH[10], equals(4043))
expect_that(res$MPH[11], equals(3484))
expect_that(res$MPH[12], equals(15436.5))
expect_that(res$MPH[13], equals(7526))
expect_that(res$MPH[14], equals(8814.5))
expect_that(res$MPH[15], equals(7084))
expect_that(res$MPH[16], equals(5167.5))
expect_that(res$MPH[17], equals(4904))
expect_that(res$MPH[18], equals(12202.5))
expect_that(res$MPH[19], equals(13938.5))
expect_that(res$MPH[20], equals(10096))
expect_that(res$MPH[21], equals(9772))
expect_that(res$MPH[22], equals(3406))
# Check result: Allele repeat difference.
expect_that(res$Delta[1], equals(1))
expect_that(res$Delta[2], equals(1))
expect_that(res$Delta[3], equals(2))
expect_that(res$Delta[4], equals(3))
expect_that(res$Delta[5], equals(2))
expect_that(res$Delta[6], equals(1))
expect_that(res$Delta[7], equals(1))
expect_that(res$Delta[8], equals(3))
expect_that(res$Delta[9], equals(3))
expect_that(res$Delta[10], equals(1))
expect_that(res$Delta[11], equals(2))
expect_that(res$Delta[12], equals(1))
expect_that(res$Delta[13], equals(3))
expect_that(res$Delta[14], equals(3))
expect_that(res$Delta[15], equals(2))
expect_that(res$Delta[16], equals(1))
expect_that(res$Delta[17], equals(2))
expect_that(res$Delta[18], equals(3))
expect_that(res$Delta[19], equals(2))
expect_that(res$Delta[20], equals(1))
expect_that(res$Delta[21], equals(2))
expect_that(res$Delta[22], equals(3))
})
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