context("calculateStutter") ################################################################################ # CHANGE LOG # 22.03.2019: Changed deprecated 'matches' to 'expect_match'. # # test_dir("inst/tests/") # test_file("tests/testthat/test-calculateStutter.r") # test_dir("tests/testthat") test_that("calculateStutter", { # Get test data. data(set4) data(ref4) # Get sample A2.1. setA1 <- set4[set4$Sample.Name == "03-A2.1", ] # TEST 01 ------------------------------------------------------------------- # Warn that 'Height' is not numeric. # expect_that(calculateStutter(data=setA1, ref=ref4), gives_warning()) # TEST 02 ------------------------------------------------------------------- # 1 Back, 0 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 1, forward = 0, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0264)) expect_that(round(res$Ratio[2], 4), equals(0.0889)) expect_that(round(res$Ratio[3], 4), equals(0.1216)) expect_that(round(res$Ratio[4], 4), equals(0.0768)) expect_that(round(res$Ratio[5], 4), equals(0.0961)) expect_that(round(res$Ratio[6], 4), equals(0.0417)) expect_that(round(res$Ratio[7], 4), equals(0.0782)) expect_that(round(res$Ratio[8], 4), equals(0.032)) expect_that(round(res$Ratio[9], 4), equals(0.1195)) expect_that(round(res$Ratio[10], 4), equals(0.0806)) expect_that(round(res$Ratio[11], 4), equals(0.0921)) expect_that(round(res$Ratio[12], 4), equals(0.0522)) expect_that(round(res$Ratio[13], 4), equals(0.0506)) expect_that(round(res$Ratio[14], 4), equals(0.0592)) expect_that(round(res$Ratio[15], 4), equals(0.0091)) expect_that(round(res$Ratio[16], 4), equals(0.0893)) expect_that(round(res$Ratio[17], 4), equals(0.0655)) expect_that(round(res$Ratio[18], 4), equals(0.1052)) expect_that(round(res$Ratio[19], 4), equals(0.1832)) expect_that(round(res$Ratio[20], 4), equals(0.0525)) expect_that(round(res$Ratio[21], 4), equals(0.0804)) expect_that(round(res$Ratio[22], 4), equals(0.0044)) expect_that(round(res$Ratio[23], 4), equals(0.0801)) expect_that(round(res$Ratio[24], 4), equals(0.0493)) expect_that(round(res$Ratio[25], 4), equals(0.1376)) # Check result: Type. expect_that(res$Type[1], equals(-1)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-1)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(-1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(-0.8)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(-1)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-1)) expect_that(res$Type[22], equals(-0.8)) expect_that(res$Type[23], equals(-1)) expect_that(res$Type[24], equals(-0.8)) expect_that(res$Type[25], equals(-1)) # TEST 03 ------------------------------------------------------------------- # 1 Back, 1 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 1, forward = 1, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0264)) expect_that(round(res$Ratio[2], 4), equals(0.0889)) expect_that(round(res$Ratio[3], 4), equals(0.0185)) expect_that(round(res$Ratio[4], 4), equals(0.1216)) expect_that(round(res$Ratio[5], 4), equals(0.0142)) expect_that(round(res$Ratio[6], 4), equals(0.0768)) expect_that(round(res$Ratio[7], 4), equals(0.0961)) expect_that(round(res$Ratio[8], 4), equals(0.0417)) expect_that(round(res$Ratio[9], 4), equals(0.009)) expect_that(round(res$Ratio[10], 4), equals(0.0782)) expect_that(round(res$Ratio[11], 4), equals(0.0086)) expect_that(round(res$Ratio[12], 4), equals(0.032)) expect_that(round(res$Ratio[13], 4), equals(0.0136)) expect_that(round(res$Ratio[14], 4), equals(0.1195)) expect_that(round(res$Ratio[15], 4), equals(0.0624)) expect_that(round(res$Ratio[16], 4), equals(0.0806)) expect_that(round(res$Ratio[17], 4), equals(0.0522)) expect_that(round(res$Ratio[18], 4), equals(0.0064)) expect_that(round(res$Ratio[19], 4), equals(0.0506)) expect_that(round(res$Ratio[20], 4), equals(0.0053)) expect_that(round(res$Ratio[21], 4), equals(0.0592)) expect_that(round(res$Ratio[22], 4), equals(0.0091)) expect_that(round(res$Ratio[23], 4), equals(0.0053)) expect_that(round(res$Ratio[24], 4), equals(0.0893)) expect_that(round(res$Ratio[25], 4), equals(0.0078)) expect_that(round(res$Ratio[26], 4), equals(0.0057)) expect_that(round(res$Ratio[27], 4), equals(0.0655)) expect_that(round(res$Ratio[28], 4), equals(0.0116)) expect_that(round(res$Ratio[29], 4), equals(0.1052)) expect_that(round(res$Ratio[30], 4), equals(0.0038)) expect_that(round(res$Ratio[31], 4), equals(0.1832)) expect_that(round(res$Ratio[32], 4), equals(0.0525)) expect_that(round(res$Ratio[33], 4), equals(0.0044)) expect_that(round(res$Ratio[34], 4), equals(0.0801)) expect_that(round(res$Ratio[35], 4), equals(0.0493)) expect_that(round(res$Ratio[36], 4), equals(0.0046)) expect_that(round(res$Ratio[37], 4), equals(0.1376)) expect_that(round(res$Ratio[38], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-1)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(-1)) expect_that(res$Type[20], equals(1)) expect_that(res$Type[21], equals(-1)) expect_that(res$Type[22], equals(-0.8)) expect_that(res$Type[23], equals(1)) expect_that(res$Type[24], equals(-1)) expect_that(res$Type[25], equals(1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(1)) expect_that(res$Type[29], equals(-1)) expect_that(res$Type[30], equals(1)) expect_that(res$Type[31], equals(-1)) expect_that(res$Type[32], equals(-1)) expect_that(res$Type[33], equals(-0.8)) expect_that(res$Type[34], equals(-1)) expect_that(res$Type[35], equals(-0.8)) expect_that(res$Type[36], equals(1)) expect_that(res$Type[37], equals(-1)) expect_that(res$Type[38], equals(1)) # TEST 04 ------------------------------------------------------------------- # 1 Back, 2 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 1, forward = 2, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0264)) expect_that(round(res$Ratio[2], 4), equals(0.0889)) expect_that(round(res$Ratio[3], 4), equals(0.0185)) expect_that(round(res$Ratio[4], 4), equals(0.0142)) expect_that(round(res$Ratio[5], 4), equals(0.0768)) expect_that(round(res$Ratio[6], 4), equals(0.0961)) expect_that(round(res$Ratio[7], 4), equals(0.0417)) expect_that(round(res$Ratio[8], 4), equals(0.009)) expect_that(round(res$Ratio[9], 4), equals(0.0086)) expect_that(round(res$Ratio[10], 4), equals(0.032)) expect_that(round(res$Ratio[11], 4), equals(0.0136)) expect_that(round(res$Ratio[12], 4), equals(0.1195)) expect_that(round(res$Ratio[13], 4), equals(0.0624)) expect_that(round(res$Ratio[14], 4), equals(0.0806)) expect_that(round(res$Ratio[15], 4), equals(0.0522)) expect_that(round(res$Ratio[16], 4), equals(0.0064)) expect_that(round(res$Ratio[17], 4), equals(0.0053)) expect_that(round(res$Ratio[18], 4), equals(0.0592)) expect_that(round(res$Ratio[19], 4), equals(0.0091)) expect_that(round(res$Ratio[20], 4), equals(0.0053)) expect_that(round(res$Ratio[21], 4), equals(0.0095)) expect_that(round(res$Ratio[22], 4), equals(0.0893)) expect_that(round(res$Ratio[23], 4), equals(0.0078)) expect_that(round(res$Ratio[24], 4), equals(0.0057)) expect_that(round(res$Ratio[25], 4), equals(0.0116)) expect_that(round(res$Ratio[26], 4), equals(0.1052)) expect_that(round(res$Ratio[27], 4), equals(0.0038)) expect_that(round(res$Ratio[28], 4), equals(0.011)) expect_that(round(res$Ratio[29], 4), equals(0.1832)) expect_that(round(res$Ratio[30], 4), equals(0.0525)) expect_that(round(res$Ratio[31], 4), equals(0.0801)) expect_that(round(res$Ratio[32], 4), equals(0.0493)) expect_that(round(res$Ratio[33], 4), equals(0.0046)) expect_that(round(res$Ratio[34], 4), equals(0.1376)) expect_that(round(res$Ratio[35], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-1)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(-0.8)) expect_that(res$Type[20], equals(1)) expect_that(res$Type[21], equals(2)) expect_that(res$Type[22], equals(-1)) expect_that(res$Type[23], equals(1)) expect_that(res$Type[24], equals(1)) expect_that(res$Type[25], equals(1)) expect_that(res$Type[26], equals(-1)) expect_that(res$Type[27], equals(1)) expect_that(res$Type[28], equals(2)) expect_that(res$Type[29], equals(-1)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(-1)) expect_that(res$Type[32], equals(-0.8)) expect_that(res$Type[33], equals(1)) expect_that(res$Type[34], equals(-1)) expect_that(res$Type[35], equals(1)) # TEST 04 ------------------------------------------------------------------- # 1 Back, 3 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 1, forward = 3, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0264)) expect_that(round(res$Ratio[2], 4), equals(0.0889)) expect_that(round(res$Ratio[3], 4), equals(0.0185)) expect_that(round(res$Ratio[4], 4), equals(0.0768)) expect_that(round(res$Ratio[5], 4), equals(0.0961)) expect_that(round(res$Ratio[6], 4), equals(0.0417)) expect_that(round(res$Ratio[7], 4), equals(0.009)) expect_that(round(res$Ratio[8], 4), equals(0.032)) expect_that(round(res$Ratio[9], 4), equals(0.0136)) expect_that(round(res$Ratio[10], 4), equals(0.0082)) expect_that(round(res$Ratio[11], 4), equals(0.1195)) expect_that(round(res$Ratio[12], 4), equals(0.0624)) expect_that(round(res$Ratio[13], 4), equals(0.0806)) expect_that(round(res$Ratio[14], 4), equals(0.0522)) expect_that(round(res$Ratio[15], 4), equals(0.0064)) expect_that(round(res$Ratio[16], 4), equals(0.0592)) expect_that(round(res$Ratio[17], 4), equals(0.0091)) expect_that(round(res$Ratio[18], 4), equals(0.0053)) expect_that(round(res$Ratio[19], 4), equals(0.0095)) expect_that(round(res$Ratio[20], 4), equals(0.0076)) expect_that(round(res$Ratio[21], 4), equals(0.0078)) expect_that(round(res$Ratio[22], 4), equals(0.0057)) expect_that(round(res$Ratio[23], 4), equals(0.1052)) expect_that(round(res$Ratio[24], 4), equals(0.0038)) expect_that(round(res$Ratio[25], 4), equals(0.011)) expect_that(round(res$Ratio[26], 4), equals(0.0525)) expect_that(round(res$Ratio[27], 4), equals(0.0801)) expect_that(round(res$Ratio[28], 4), equals(0.0493)) expect_that(round(res$Ratio[29], 4), equals(0.0046)) expect_that(round(res$Ratio[30], 4), equals(0.1376)) expect_that(round(res$Ratio[31], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-1)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(3)) expect_that(res$Type[11], equals(-1)) expect_that(res$Type[12], equals(1)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(-0.8)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(2)) expect_that(res$Type[20], equals(2.2)) expect_that(res$Type[21], equals(1)) expect_that(res$Type[22], equals(1)) expect_that(res$Type[23], equals(-1)) expect_that(res$Type[24], equals(1)) expect_that(res$Type[25], equals(2)) expect_that(res$Type[26], equals(-1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(-0.8)) expect_that(res$Type[29], equals(1)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(1)) # TEST 05 ------------------------------------------------------------------- # 2 Back, 0 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 0, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.0243)) expect_that(round(res$Ratio[6], 4), equals(0.1216)) expect_that(round(res$Ratio[7], 4), equals(0.0768)) expect_that(round(res$Ratio[8], 4), equals(0.0961)) expect_that(round(res$Ratio[9], 4), equals(0.0417)) expect_that(round(res$Ratio[10], 4), equals(0.009)) expect_that(round(res$Ratio[11], 4), equals(0.0782)) expect_that(round(res$Ratio[12], 4), equals(0.032)) expect_that(round(res$Ratio[13], 4), equals(0.0093)) expect_that(round(res$Ratio[14], 4), equals(0.1195)) expect_that(round(res$Ratio[15], 4), equals(0.0921)) expect_that(round(res$Ratio[16], 4), equals(0.0522)) expect_that(round(res$Ratio[17], 4), equals(0.0067)) expect_that(round(res$Ratio[18], 4), equals(0.0506)) expect_that(round(res$Ratio[19], 4), equals(0.0592)) expect_that(round(res$Ratio[20], 4), equals(0.0091)) expect_that(round(res$Ratio[21], 4), equals(0.0097)) expect_that(round(res$Ratio[22], 4), equals(0.0078)) expect_that(round(res$Ratio[23], 4), equals(0.0893)) expect_that(round(res$Ratio[24], 4), equals(0.0057)) expect_that(round(res$Ratio[25], 4), equals(0.0655)) expect_that(round(res$Ratio[26], 4), equals(0.0062)) expect_that(round(res$Ratio[27], 4), equals(0.1052)) expect_that(round(res$Ratio[28], 4), equals(0.015)) expect_that(round(res$Ratio[29], 4), equals(0.1832)) expect_that(round(res$Ratio[30], 4), equals(0.0804)) expect_that(round(res$Ratio[31], 4), equals(0.0044)) expect_that(round(res$Ratio[32], 4), equals(0.0054)) expect_that(round(res$Ratio[33], 4), equals(0.006)) expect_that(round(res$Ratio[34], 4), equals(0.0801)) expect_that(round(res$Ratio[35], 4), equals(0.0493)) expect_that(round(res$Ratio[36], 4), equals(0.0099)) expect_that(round(res$Ratio[37], 4), equals(0.1376)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-2)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-2)) expect_that(res$Type[11], equals(-1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(-2)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(-2)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(-1)) expect_that(res$Type[20], equals(-0.8)) expect_that(res$Type[21], equals(-2)) expect_that(res$Type[22], equals(-1.8)) expect_that(res$Type[23], equals(-1)) expect_that(res$Type[24], equals(-1.7)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(-2)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(-2)) expect_that(res$Type[29], equals(-1)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(-0.8)) expect_that(res$Type[32], equals(-2)) expect_that(res$Type[33], equals(-1.8)) expect_that(res$Type[34], equals(-1)) expect_that(res$Type[35], equals(-0.8)) expect_that(res$Type[36], equals(-2)) expect_that(res$Type[37], equals(-1)) # TEST 06 ------------------------------------------------------------------- # 2 Back, 1 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 1, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.1216)) expect_that(round(res$Ratio[6], 4), equals(0.0142)) expect_that(round(res$Ratio[7], 4), equals(0.0768)) expect_that(round(res$Ratio[8], 4), equals(0.0961)) expect_that(round(res$Ratio[9], 4), equals(0.0417)) expect_that(round(res$Ratio[10], 4), equals(0.0782)) expect_that(round(res$Ratio[11], 4), equals(0.0086)) expect_that(round(res$Ratio[12], 4), equals(0.032)) expect_that(round(res$Ratio[13], 4), equals(0.0136)) expect_that(round(res$Ratio[14], 4), equals(0.0093)) expect_that(round(res$Ratio[15], 4), equals(0.1195)) expect_that(round(res$Ratio[16], 4), equals(0.0624)) expect_that(round(res$Ratio[17], 4), equals(0.0522)) expect_that(round(res$Ratio[18], 4), equals(0.0506)) expect_that(round(res$Ratio[19], 4), equals(0.0053)) expect_that(round(res$Ratio[20], 4), equals(0.0592)) expect_that(round(res$Ratio[21], 4), equals(0.0091)) expect_that(round(res$Ratio[22], 4), equals(0.0053)) expect_that(round(res$Ratio[23], 4), equals(0.0097)) expect_that(round(res$Ratio[24], 4), equals(0.0078)) expect_that(round(res$Ratio[25], 4), equals(0.0893)) expect_that(round(res$Ratio[26], 4), equals(0.0078)) expect_that(round(res$Ratio[27], 4), equals(0.0655)) expect_that(round(res$Ratio[28], 4), equals(0.0116)) expect_that(round(res$Ratio[29], 4), equals(0.0062)) expect_that(round(res$Ratio[30], 4), equals(0.1052)) expect_that(round(res$Ratio[31], 4), equals(0.0038)) expect_that(round(res$Ratio[32], 4), equals(0.015)) expect_that(round(res$Ratio[33], 4), equals(0.1832)) expect_that(round(res$Ratio[34], 4), equals(0.0044)) expect_that(round(res$Ratio[35], 4), equals(0.0054)) expect_that(round(res$Ratio[36], 4), equals(0.006)) expect_that(round(res$Ratio[37], 4), equals(0.0801)) expect_that(round(res$Ratio[38], 4), equals(0.0493)) expect_that(round(res$Ratio[39], 4), equals(0.0046)) expect_that(round(res$Ratio[40], 4), equals(0.0099)) expect_that(round(res$Ratio[41], 4), equals(0.1376)) expect_that(round(res$Ratio[42], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-2)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-0.8)) expect_that(res$Type[22], equals(1)) expect_that(res$Type[23], equals(-2)) expect_that(res$Type[24], equals(-1.8)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(1)) expect_that(res$Type[29], equals(-2)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(1)) expect_that(res$Type[32], equals(-2)) expect_that(res$Type[33], equals(-1)) expect_that(res$Type[34], equals(-0.8)) expect_that(res$Type[35], equals(-2)) expect_that(res$Type[36], equals(-1.8)) expect_that(res$Type[37], equals(-1)) expect_that(res$Type[38], equals(-0.8)) expect_that(res$Type[39], equals(1)) expect_that(res$Type[40], equals(-2)) expect_that(res$Type[41], equals(-1)) expect_that(res$Type[42], equals(1)) # TEST 07 ------------------------------------------------------------------- # 2 Back, 2 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 2, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.0142)) expect_that(round(res$Ratio[6], 4), equals(0.0768)) expect_that(round(res$Ratio[7], 4), equals(0.0961)) expect_that(round(res$Ratio[8], 4), equals(0.0417)) expect_that(round(res$Ratio[9], 4), equals(0.0086)) expect_that(round(res$Ratio[10], 4), equals(0.032)) expect_that(round(res$Ratio[11], 4), equals(0.0136)) expect_that(round(res$Ratio[12], 4), equals(0.0093)) expect_that(round(res$Ratio[13], 4), equals(0.1195)) expect_that(round(res$Ratio[14], 4), equals(0.0624)) expect_that(round(res$Ratio[15], 4), equals(0.0522)) expect_that(round(res$Ratio[16], 4), equals(0.0053)) expect_that(round(res$Ratio[17], 4), equals(0.0592)) expect_that(round(res$Ratio[18], 4), equals(0.0091)) expect_that(round(res$Ratio[19], 4), equals(0.0053)) expect_that(round(res$Ratio[20], 4), equals(0.0078)) expect_that(round(res$Ratio[21], 4), equals(0.0893)) expect_that(round(res$Ratio[22], 4), equals(0.0078)) expect_that(round(res$Ratio[23], 4), equals(0.0116)) expect_that(round(res$Ratio[24], 4), equals(0.0062)) expect_that(round(res$Ratio[25], 4), equals(0.1052)) expect_that(round(res$Ratio[26], 4), equals(0.0038)) expect_that(round(res$Ratio[27], 4), equals(0.1832)) expect_that(round(res$Ratio[28], 4), equals(0.0054)) expect_that(round(res$Ratio[29], 4), equals(0.006)) expect_that(round(res$Ratio[30], 4), equals(0.0801)) expect_that(round(res$Ratio[31], 4), equals(0.0493)) expect_that(round(res$Ratio[32], 4), equals(0.0046)) expect_that(round(res$Ratio[33], 4), equals(0.0099)) expect_that(round(res$Ratio[34], 4), equals(0.1376)) expect_that(round(res$Ratio[35], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-2)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(1)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(-0.8)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(-1.8)) expect_that(res$Type[21], equals(-1)) expect_that(res$Type[22], equals(1)) expect_that(res$Type[23], equals(1)) expect_that(res$Type[24], equals(-2)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(-2)) expect_that(res$Type[29], equals(-1.8)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(-0.8)) expect_that(res$Type[32], equals(1)) expect_that(res$Type[33], equals(-2)) expect_that(res$Type[34], equals(-1)) expect_that(res$Type[35], equals(1)) # TEST 08 ------------------------------------------------------------------- # 2 Back, 3 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 3, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.0768)) expect_that(round(res$Ratio[6], 4), equals(0.0961)) expect_that(round(res$Ratio[7], 4), equals(0.0417)) expect_that(round(res$Ratio[8], 4), equals(0.032)) expect_that(round(res$Ratio[9], 4), equals(0.0136)) expect_that(round(res$Ratio[10], 4), equals(0.1195)) expect_that(round(res$Ratio[11], 4), equals(0.0624)) expect_that(round(res$Ratio[12], 4), equals(0.0522)) expect_that(round(res$Ratio[13], 4), equals(0.0592)) expect_that(round(res$Ratio[14], 4), equals(0.0091)) expect_that(round(res$Ratio[15], 4), equals(0.0053)) expect_that(round(res$Ratio[16], 4), equals(0.0078)) expect_that(round(res$Ratio[17], 4), equals(0.0062)) expect_that(round(res$Ratio[18], 4), equals(0.1052)) expect_that(round(res$Ratio[19], 4), equals(0.0038)) expect_that(round(res$Ratio[20], 4), equals(0.0054)) expect_that(round(res$Ratio[21], 4), equals(0.006)) expect_that(round(res$Ratio[22], 4), equals(0.0801)) expect_that(round(res$Ratio[23], 4), equals(0.0493)) expect_that(round(res$Ratio[24], 4), equals(0.0046)) expect_that(round(res$Ratio[25], 4), equals(0.0099)) expect_that(round(res$Ratio[26], 4), equals(0.1376)) expect_that(round(res$Ratio[27], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(-0.8)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(-2)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(-2)) expect_that(res$Type[21], equals(-1.8)) expect_that(res$Type[22], equals(-1)) expect_that(res$Type[23], equals(-0.8)) expect_that(res$Type[24], equals(1)) expect_that(res$Type[25], equals(-2)) expect_that(res$Type[26], equals(-1)) expect_that(res$Type[27], equals(1)) # TEST 09 ------------------------------------------------------------------- # 3 Back, 0 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 3, forward = 0, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0243)) expect_that(round(res$Ratio[4], 4), equals(0.1216)) expect_that(round(res$Ratio[5], 4), equals(0.0768)) expect_that(round(res$Ratio[6], 4), equals(0.0961)) expect_that(round(res$Ratio[7], 4), equals(0.009)) expect_that(round(res$Ratio[8], 4), equals(0.0782)) expect_that(round(res$Ratio[9], 4), equals(0.032)) expect_that(round(res$Ratio[10], 4), equals(0.0093)) expect_that(round(res$Ratio[11], 4), equals(0.1195)) expect_that(round(res$Ratio[12], 4), equals(0.0921)) expect_that(round(res$Ratio[13], 4), equals(0.0067)) expect_that(round(res$Ratio[14], 4), equals(0.0506)) expect_that(round(res$Ratio[15], 4), equals(0.0592)) expect_that(round(res$Ratio[16], 4), equals(0.0091)) expect_that(round(res$Ratio[17], 4), equals(0.0054)) expect_that(round(res$Ratio[18], 4), equals(0.0097)) expect_that(round(res$Ratio[19], 4), equals(0.0078)) expect_that(round(res$Ratio[20], 4), equals(0.0893)) expect_that(round(res$Ratio[21], 4), equals(0.0057)) expect_that(round(res$Ratio[22], 4), equals(0.0655)) expect_that(round(res$Ratio[23], 4), equals(0.0062)) expect_that(round(res$Ratio[24], 4), equals(0.1052)) expect_that(round(res$Ratio[25], 4), equals(0.0052)) expect_that(round(res$Ratio[26], 4), equals(0.015)) expect_that(round(res$Ratio[27], 4), equals(0.1832)) expect_that(round(res$Ratio[28], 4), equals(0.0804)) expect_that(round(res$Ratio[29], 4), equals(0.0044)) expect_that(round(res$Ratio[30], 4), equals(0.0054)) expect_that(round(res$Ratio[31], 4), equals(0.006)) expect_that(round(res$Ratio[32], 4), equals(0.0801)) expect_that(round(res$Ratio[33], 4), equals(0.0493)) expect_that(round(res$Ratio[34], 4), equals(0.0099)) expect_that(round(res$Ratio[35], 4), equals(0.1376)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-2)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-2)) expect_that(res$Type[11], equals(-1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(-2)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(-0.8)) expect_that(res$Type[17], equals(-3)) expect_that(res$Type[18], equals(-2)) expect_that(res$Type[19], equals(-1.8)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-1.7)) expect_that(res$Type[22], equals(-1)) expect_that(res$Type[23], equals(-2)) expect_that(res$Type[24], equals(-1)) expect_that(res$Type[25], equals(-3)) expect_that(res$Type[26], equals(-2)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(-1)) expect_that(res$Type[29], equals(-0.8)) expect_that(res$Type[30], equals(-2)) expect_that(res$Type[31], equals(-1.8)) expect_that(res$Type[32], equals(-1)) expect_that(res$Type[33], equals(-0.8)) expect_that(res$Type[34], equals(-2)) expect_that(res$Type[35], equals(-1)) # TEST 10 ------------------------------------------------------------------- # 3 Back, 1 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 3, forward = 1, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.1216)) expect_that(round(res$Ratio[4], 4), equals(0.0142)) expect_that(round(res$Ratio[5], 4), equals(0.0768)) expect_that(round(res$Ratio[6], 4), equals(0.0961)) expect_that(round(res$Ratio[7], 4), equals(0.0782)) expect_that(round(res$Ratio[8], 4), equals(0.0086)) expect_that(round(res$Ratio[9], 4), equals(0.032)) expect_that(round(res$Ratio[10], 4), equals(0.0136)) expect_that(round(res$Ratio[11], 4), equals(0.0093)) expect_that(round(res$Ratio[12], 4), equals(0.1195)) expect_that(round(res$Ratio[13], 4), equals(0.0624)) expect_that(round(res$Ratio[14], 4), equals(0.0506)) expect_that(round(res$Ratio[15], 4), equals(0.0053)) expect_that(round(res$Ratio[16], 4), equals(0.0592)) expect_that(round(res$Ratio[17], 4), equals(0.0091)) expect_that(round(res$Ratio[18], 4), equals(0.0097)) expect_that(round(res$Ratio[19], 4), equals(0.0078)) expect_that(round(res$Ratio[20], 4), equals(0.0893)) expect_that(round(res$Ratio[21], 4), equals(0.0078)) expect_that(round(res$Ratio[22], 4), equals(0.0655)) expect_that(round(res$Ratio[23], 4), equals(0.0116)) expect_that(round(res$Ratio[24], 4), equals(0.0062)) expect_that(round(res$Ratio[25], 4), equals(0.1052)) expect_that(round(res$Ratio[26], 4), equals(0.015)) expect_that(round(res$Ratio[27], 4), equals(0.1832)) expect_that(round(res$Ratio[28], 4), equals(0.0044)) expect_that(round(res$Ratio[29], 4), equals(0.0054)) expect_that(round(res$Ratio[30], 4), equals(0.006)) expect_that(round(res$Ratio[31], 4), equals(0.0801)) expect_that(round(res$Ratio[32], 4), equals(0.0493)) expect_that(round(res$Ratio[33], 4), equals(0.0046)) expect_that(round(res$Ratio[34], 4), equals(0.0099)) expect_that(round(res$Ratio[35], 4), equals(0.1376)) expect_that(round(res$Ratio[36], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-1)) expect_that(res$Type[4], equals(1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(1)) expect_that(res$Type[11], equals(-2)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(-0.8)) expect_that(res$Type[18], equals(-2)) expect_that(res$Type[19], equals(-1.8)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(1)) expect_that(res$Type[22], equals(-1)) expect_that(res$Type[23], equals(1)) expect_that(res$Type[24], equals(-2)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(-2)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(-0.8)) expect_that(res$Type[29], equals(-2)) expect_that(res$Type[30], equals(-1.8)) expect_that(res$Type[31], equals(-1)) expect_that(res$Type[32], equals(-0.8)) expect_that(res$Type[33], equals(1)) expect_that(res$Type[34], equals(-2)) expect_that(res$Type[35], equals(-1)) expect_that(res$Type[36], equals(1)) # TEST 11 ------------------------------------------------------------------- # 3 Back, 2 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 3, forward = 2, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0142)) expect_that(round(res$Ratio[4], 4), equals(0.0768)) expect_that(round(res$Ratio[5], 4), equals(0.0961)) expect_that(round(res$Ratio[6], 4), equals(0.0086)) expect_that(round(res$Ratio[7], 4), equals(0.032)) expect_that(round(res$Ratio[8], 4), equals(0.0136)) expect_that(round(res$Ratio[9], 4), equals(0.0093)) expect_that(round(res$Ratio[10], 4), equals(0.1195)) expect_that(round(res$Ratio[11], 4), equals(0.0624)) expect_that(round(res$Ratio[12], 4), equals(0.0053)) expect_that(round(res$Ratio[13], 4), equals(0.0592)) expect_that(round(res$Ratio[14], 4), equals(0.0091)) expect_that(round(res$Ratio[15], 4), equals(0.0078)) expect_that(round(res$Ratio[16], 4), equals(0.0893)) expect_that(round(res$Ratio[17], 4), equals(0.0078)) expect_that(round(res$Ratio[18], 4), equals(0.0116)) expect_that(round(res$Ratio[19], 4), equals(0.0062)) expect_that(round(res$Ratio[20], 4), equals(0.1052)) expect_that(round(res$Ratio[21], 4), equals(0.1832)) expect_that(round(res$Ratio[22], 4), equals(0.0054)) expect_that(round(res$Ratio[23], 4), equals(0.006)) expect_that(round(res$Ratio[24], 4), equals(0.0801)) expect_that(round(res$Ratio[25], 4), equals(0.0493)) expect_that(round(res$Ratio[26], 4), equals(0.0046)) expect_that(round(res$Ratio[27], 4), equals(0.0099)) expect_that(round(res$Ratio[28], 4), equals(0.1376)) expect_that(round(res$Ratio[29], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(-2)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(1)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(-0.8)) expect_that(res$Type[15], equals(-1.8)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(1)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(-2)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-1)) expect_that(res$Type[22], equals(-2)) expect_that(res$Type[23], equals(-1.8)) expect_that(res$Type[24], equals(-1)) expect_that(res$Type[25], equals(-0.8)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-2)) expect_that(res$Type[28], equals(-1)) expect_that(res$Type[29], equals(1)) # TEST 12 ------------------------------------------------------------------- # 3 Back, 3 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 3, forward = 3, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0768)) expect_that(round(res$Ratio[4], 4), equals(0.0961)) expect_that(round(res$Ratio[5], 4), equals(0.032)) expect_that(round(res$Ratio[6], 4), equals(0.0136)) expect_that(round(res$Ratio[7], 4), equals(0.1195)) expect_that(round(res$Ratio[8], 4), equals(0.0624)) expect_that(round(res$Ratio[9], 4), equals(0.0592)) expect_that(round(res$Ratio[10], 4), equals(0.0091)) expect_that(round(res$Ratio[11], 4), equals(0.0078)) expect_that(round(res$Ratio[12], 4), equals(0.0062)) expect_that(round(res$Ratio[13], 4), equals(0.1052)) expect_that(round(res$Ratio[14], 4), equals(0.0054)) expect_that(round(res$Ratio[15], 4), equals(0.006)) expect_that(round(res$Ratio[16], 4), equals(0.0801)) expect_that(round(res$Ratio[17], 4), equals(0.0493)) expect_that(round(res$Ratio[18], 4), equals(0.0046)) expect_that(round(res$Ratio[19], 4), equals(0.0099)) expect_that(round(res$Ratio[20], 4), equals(0.1376)) expect_that(round(res$Ratio[21], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-1)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-0.8)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-2)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(-2)) expect_that(res$Type[15], equals(-1.8)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(-0.8)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(-2)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(1)) # TEST 13 ------------------------------------------------------------------- # 0 Back, 1 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 0, forward = 1, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0185)) expect_that(round(res$Ratio[2], 4), equals(0.0142)) expect_that(round(res$Ratio[3], 4), equals(0.009)) expect_that(round(res$Ratio[4], 4), equals(0.0086)) expect_that(round(res$Ratio[5], 4), equals(0.0136)) expect_that(round(res$Ratio[6], 4), equals(0.0624)) expect_that(round(res$Ratio[7], 4), equals(0.083)) expect_that(round(res$Ratio[8], 4), equals(0.0064)) expect_that(round(res$Ratio[9], 4), equals(0.0053)) expect_that(round(res$Ratio[10], 4), equals(0.0053)) expect_that(round(res$Ratio[11], 4), equals(0.0078)) expect_that(round(res$Ratio[12], 4), equals(0.0057)) expect_that(round(res$Ratio[13], 4), equals(0.0116)) expect_that(round(res$Ratio[14], 4), equals(0.0038)) expect_that(round(res$Ratio[15], 4), equals(0.0967)) expect_that(round(res$Ratio[16], 4), equals(0.0046)) expect_that(round(res$Ratio[17], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(1)) expect_that(res$Type[2], equals(1)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(1)) expect_that(res$Type[5], equals(1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(1)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(1)) # TEST 14 ------------------------------------------------------------------- # 0 Back, 2 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 0, forward = 2, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0185)) expect_that(round(res$Ratio[2], 4), equals(0.0927)) expect_that(round(res$Ratio[3], 4), equals(0.0142)) expect_that(round(res$Ratio[4], 4), equals(0.009)) expect_that(round(res$Ratio[5], 4), equals(0.0779)) expect_that(round(res$Ratio[6], 4), equals(0.0086)) expect_that(round(res$Ratio[7], 4), equals(0.0136)) expect_that(round(res$Ratio[8], 4), equals(0.0624)) expect_that(round(res$Ratio[9], 4), equals(0.083)) expect_that(round(res$Ratio[10], 4), equals(0.0064)) expect_that(round(res$Ratio[11], 4), equals(0.0486)) expect_that(round(res$Ratio[12], 4), equals(0.0053)) expect_that(round(res$Ratio[13], 4), equals(0.0053)) expect_that(round(res$Ratio[14], 4), equals(0.0095)) expect_that(round(res$Ratio[15], 4), equals(0.0078)) expect_that(round(res$Ratio[16], 4), equals(0.0057)) expect_that(round(res$Ratio[17], 4), equals(0.0655)) expect_that(round(res$Ratio[18], 4), equals(0.0116)) expect_that(round(res$Ratio[19], 4), equals(0.0038)) expect_that(round(res$Ratio[20], 4), equals(0.011)) expect_that(round(res$Ratio[21], 4), equals(0.0967)) expect_that(round(res$Ratio[22], 4), equals(0.0053)) expect_that(round(res$Ratio[23], 4), equals(0.0046)) expect_that(round(res$Ratio[24], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(1)) expect_that(res$Type[2], equals(2)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(1)) expect_that(res$Type[5], equals(2)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(1)) expect_that(res$Type[11], equals(2)) expect_that(res$Type[12], equals(1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(2)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(1.7)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(2)) expect_that(res$Type[21], equals(1)) expect_that(res$Type[22], equals(1.2)) expect_that(res$Type[23], equals(1)) expect_that(res$Type[24], equals(1)) # TEST 15 ------------------------------------------------------------------- # 0 Back, 3 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 0, forward = 3, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0185)) expect_that(round(res$Ratio[2], 4), equals(0.0927)) expect_that(round(res$Ratio[3], 4), equals(0.009)) expect_that(round(res$Ratio[4], 4), equals(0.0779)) expect_that(round(res$Ratio[5], 4), equals(0.0136)) expect_that(round(res$Ratio[6], 4), equals(0.0082)) expect_that(round(res$Ratio[7], 4), equals(0.0624)) expect_that(round(res$Ratio[8], 4), equals(0.083)) expect_that(round(res$Ratio[9], 4), equals(0.0064)) expect_that(round(res$Ratio[10], 4), equals(0.0486)) expect_that(round(res$Ratio[11], 4), equals(0.0053)) expect_that(round(res$Ratio[12], 4), equals(0.0095)) expect_that(round(res$Ratio[13], 4), equals(0.0076)) expect_that(round(res$Ratio[14], 4), equals(0.0871)) expect_that(round(res$Ratio[15], 4), equals(0.0078)) expect_that(round(res$Ratio[16], 4), equals(0.0057)) expect_that(round(res$Ratio[17], 4), equals(0.0655)) expect_that(round(res$Ratio[18], 4), equals(0.0038)) expect_that(round(res$Ratio[19], 4), equals(0.011)) expect_that(round(res$Ratio[20], 4), equals(0.1344)) expect_that(round(res$Ratio[21], 4), equals(0.0967)) expect_that(round(res$Ratio[22], 4), equals(0.0053)) expect_that(round(res$Ratio[23], 4), equals(0.0046)) expect_that(round(res$Ratio[24], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(1)) expect_that(res$Type[2], equals(2)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(2)) expect_that(res$Type[5], equals(1)) expect_that(res$Type[6], equals(3)) expect_that(res$Type[7], equals(1)) expect_that(res$Type[8], equals(1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(2)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(2)) expect_that(res$Type[13], equals(2.2)) expect_that(res$Type[14], equals(3)) expect_that(res$Type[15], equals(1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(1.7)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(2)) expect_that(res$Type[20], equals(3)) expect_that(res$Type[21], equals(1)) expect_that(res$Type[22], equals(1.2)) expect_that(res$Type[23], equals(1)) expect_that(res$Type[24], equals(1)) # TEST 16 ------------------------------------------------------------------- # 2 Back, 1 Forward, stutter interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 1, interference = 1, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0074)) expect_that(round(res$Ratio[2], 4), equals(0.0742)) expect_that(round(res$Ratio[3], 4), equals(0.0067)) expect_that(round(res$Ratio[4], 4), equals(0.0035)) expect_that(round(res$Ratio[5], 4), equals(0.0264)) expect_that(round(res$Ratio[6], 4), equals(0.0637)) expect_that(round(res$Ratio[7], 4), equals(0.0076)) expect_that(round(res$Ratio[8], 4), equals(0.0697)) expect_that(round(res$Ratio[9], 4), equals(0.0136)) expect_that(round(res$Ratio[10], 4), equals(0.0064)) expect_that(round(res$Ratio[11], 4), equals(0.0895)) expect_that(round(res$Ratio[12], 4), equals(0.0062)) expect_that(round(res$Ratio[13], 4), equals(0.0889)) expect_that(round(res$Ratio[14], 4), equals(0.0185)) expect_that(round(res$Ratio[15], 4), equals(0.0243)) expect_that(round(res$Ratio[16], 4), equals(0.1216)) expect_that(round(res$Ratio[17], 4), equals(0.0142)) expect_that(round(res$Ratio[18], 4), equals(0.0768)) expect_that(round(res$Ratio[19], 4), equals(0.0961)) expect_that(round(res$Ratio[20], 4), equals(0.0417)) expect_that(round(res$Ratio[21], 4), equals(0.009)) expect_that(round(res$Ratio[22], 4), equals(0.009)) expect_that(round(res$Ratio[23], 4), equals(0.0782)) expect_that(round(res$Ratio[24], 4), equals(0.0086)) expect_that(round(res$Ratio[25], 4), equals(0.032)) expect_that(round(res$Ratio[26], 4), equals(0.0136)) expect_that(round(res$Ratio[27], 4), equals(0.0093)) expect_that(round(res$Ratio[28], 4), equals(0.1195)) expect_that(round(res$Ratio[29], 4), equals(0.0624)) expect_that(round(res$Ratio[30], 4), equals(0.0076)) expect_that(round(res$Ratio[31], 4), equals(0.0109)) expect_that(round(res$Ratio[32], 4), equals(0.0806)) expect_that(round(res$Ratio[33], 4), equals(0.083)) expect_that(round(res$Ratio[34], 4), equals(0.0921)) expect_that(round(res$Ratio[35], 4), equals(0.0522)) expect_that(round(res$Ratio[36], 4), equals(0.0064)) expect_that(round(res$Ratio[37], 4), equals(0.0067)) expect_that(round(res$Ratio[38], 4), equals(0.0506)) expect_that(round(res$Ratio[39], 4), equals(0.0053)) expect_that(round(res$Ratio[40], 4), equals(0.0592)) expect_that(round(res$Ratio[41], 4), equals(0.0091)) expect_that(round(res$Ratio[42], 4), equals(0.0053)) expect_that(round(res$Ratio[43], 4), equals(0.0097)) expect_that(round(res$Ratio[44], 4), equals(0.0078)) expect_that(round(res$Ratio[45], 4), equals(0.0893)) expect_that(round(res$Ratio[46], 4), equals(0.0078)) expect_that(round(res$Ratio[47], 4), equals(0.0057)) expect_that(round(res$Ratio[48], 4), equals(0.0057)) expect_that(round(res$Ratio[49], 4), equals(0.0655)) expect_that(round(res$Ratio[50], 4), equals(0.0116)) expect_that(round(res$Ratio[51], 4), equals(0.0062)) expect_that(round(res$Ratio[52], 4), equals(0.1052)) expect_that(round(res$Ratio[53], 4), equals(0.0038)) expect_that(round(res$Ratio[54], 4), equals(0.015)) expect_that(round(res$Ratio[55], 4), equals(0.1832)) expect_that(round(res$Ratio[56], 4), equals(0.0525)) expect_that(round(res$Ratio[57], 4), equals(0.0967)) expect_that(round(res$Ratio[58], 4), equals(0.0804)) expect_that(round(res$Ratio[59], 4), equals(0.0044)) expect_that(round(res$Ratio[60], 4), equals(0.0054)) expect_that(round(res$Ratio[61], 4), equals(0.006)) expect_that(round(res$Ratio[62], 4), equals(0.0801)) expect_that(round(res$Ratio[63], 4), equals(0.0493)) expect_that(round(res$Ratio[64], 4), equals(0.0046)) expect_that(round(res$Ratio[65], 4), equals(0.0099)) expect_that(round(res$Ratio[66], 4), equals(0.1376)) expect_that(round(res$Ratio[67], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(1)) expect_that(res$Type[4], equals(-2)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(-2)) expect_that(res$Type[11], equals(-1)) expect_that(res$Type[12], equals(-2)) expect_that(res$Type[13], equals(-1)) expect_that(res$Type[14], equals(1)) expect_that(res$Type[15], equals(-2)) expect_that(res$Type[16], equals(-1)) expect_that(res$Type[17], equals(1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(-1)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(1)) expect_that(res$Type[22], equals(-2)) expect_that(res$Type[23], equals(-1)) expect_that(res$Type[24], equals(1)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-2)) expect_that(res$Type[28], equals(-1)) expect_that(res$Type[29], equals(1)) expect_that(res$Type[30], equals(-2)) expect_that(res$Type[31], equals(-1.8)) expect_that(res$Type[32], equals(-1)) expect_that(res$Type[33], equals(1)) expect_that(res$Type[34], equals(-1)) expect_that(res$Type[35], equals(-1)) expect_that(res$Type[36], equals(1)) expect_that(res$Type[37], equals(-2)) expect_that(res$Type[38], equals(-1)) expect_that(res$Type[39], equals(1)) expect_that(res$Type[40], equals(-1)) expect_that(res$Type[41], equals(-0.8)) expect_that(res$Type[42], equals(1)) expect_that(res$Type[43], equals(-2)) expect_that(res$Type[44], equals(-1.8)) expect_that(res$Type[45], equals(-1)) expect_that(res$Type[46], equals(1)) expect_that(res$Type[47], equals(1)) expect_that(res$Type[48], equals(-1.7)) expect_that(res$Type[49], equals(-1)) expect_that(res$Type[50], equals(1)) expect_that(res$Type[51], equals(-2)) expect_that(res$Type[52], equals(-1)) expect_that(res$Type[53], equals(1)) expect_that(res$Type[54], equals(-2)) expect_that(res$Type[55], equals(-1)) expect_that(res$Type[56], equals(-1)) expect_that(res$Type[57], equals(1)) expect_that(res$Type[58], equals(-1)) expect_that(res$Type[59], equals(-0.8)) expect_that(res$Type[60], equals(-2)) expect_that(res$Type[61], equals(-1.8)) expect_that(res$Type[62], equals(-1)) expect_that(res$Type[63], equals(-0.8)) expect_that(res$Type[64], equals(1)) expect_that(res$Type[65], equals(-2)) expect_that(res$Type[66], equals(-1)) expect_that(res$Type[67], equals(1)) # TEST 17 ------------------------------------------------------------------- # 2 Back, 1 Forward, allele interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 1, interference = 2, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0074)) expect_that(round(res$Ratio[2], 4), equals(0.0742)) expect_that(round(res$Ratio[3], 4), equals(0.0882)) expect_that(round(res$Ratio[4], 4), equals(0.0067)) expect_that(round(res$Ratio[5], 4), equals(0.0035)) expect_that(round(res$Ratio[6], 4), equals(0.0264)) expect_that(round(res$Ratio[7], 4), equals(0.0637)) expect_that(round(res$Ratio[8], 4), equals(0.0725)) expect_that(round(res$Ratio[9], 4), equals(0.0076)) expect_that(round(res$Ratio[10], 4), equals(0.0697)) expect_that(round(res$Ratio[11], 4), equals(0.0809)) expect_that(round(res$Ratio[12], 4), equals(0.0136)) expect_that(round(res$Ratio[13], 4), equals(0.0064)) expect_that(round(res$Ratio[14], 4), equals(0.0895)) expect_that(round(res$Ratio[15], 4), equals(0.099)) expect_that(round(res$Ratio[16], 4), equals(0.0062)) expect_that(round(res$Ratio[17], 4), equals(0.0889)) expect_that(round(res$Ratio[18], 4), equals(0.0185)) expect_that(round(res$Ratio[19], 4), equals(0.0243)) expect_that(round(res$Ratio[20], 4), equals(0.1216)) expect_that(round(res$Ratio[21], 4), equals(0.0142)) expect_that(round(res$Ratio[22], 4), equals(0.0768)) expect_that(round(res$Ratio[23], 4), equals(0.0961)) expect_that(round(res$Ratio[24], 4), equals(0.0417)) expect_that(round(res$Ratio[25], 4), equals(0.009)) expect_that(round(res$Ratio[26], 4), equals(0.009)) expect_that(round(res$Ratio[27], 4), equals(0.0782)) expect_that(round(res$Ratio[28], 4), equals(0.0086)) expect_that(round(res$Ratio[29], 4), equals(0.032)) expect_that(round(res$Ratio[30], 4), equals(0.0136)) expect_that(round(res$Ratio[31], 4), equals(0.0093)) expect_that(round(res$Ratio[32], 4), equals(0.1195)) expect_that(round(res$Ratio[33], 4), equals(0.0624)) expect_that(round(res$Ratio[34], 4), equals(0.0076)) expect_that(round(res$Ratio[35], 4), equals(0.0109)) expect_that(round(res$Ratio[36], 4), equals(0.0806)) expect_that(round(res$Ratio[37], 4), equals(0.083)) expect_that(round(res$Ratio[38], 4), equals(0.0921)) expect_that(round(res$Ratio[39], 4), equals(0.0522)) expect_that(round(res$Ratio[40], 4), equals(0.0064)) expect_that(round(res$Ratio[41], 4), equals(0.0067)) expect_that(round(res$Ratio[42], 4), equals(0.0506)) expect_that(round(res$Ratio[43], 4), equals(0.0053)) expect_that(round(res$Ratio[44], 4), equals(0.0592)) expect_that(round(res$Ratio[45], 4), equals(0.0091)) expect_that(round(res$Ratio[46], 4), equals(0.0053)) expect_that(round(res$Ratio[47], 4), equals(0.0097)) expect_that(round(res$Ratio[48], 4), equals(0.0078)) expect_that(round(res$Ratio[49], 4), equals(0.0893)) expect_that(round(res$Ratio[50], 4), equals(0.0078)) expect_that(round(res$Ratio[51], 4), equals(0.0057)) expect_that(round(res$Ratio[52], 4), equals(0.0057)) expect_that(round(res$Ratio[53], 4), equals(0.0655)) expect_that(round(res$Ratio[54], 4), equals(0.0116)) expect_that(round(res$Ratio[55], 4), equals(0.0062)) expect_that(round(res$Ratio[56], 4), equals(0.1052)) expect_that(round(res$Ratio[57], 4), equals(0.0038)) expect_that(round(res$Ratio[58], 4), equals(0.015)) expect_that(round(res$Ratio[59], 4), equals(0.1832)) expect_that(round(res$Ratio[60], 4), equals(0.0525)) expect_that(round(res$Ratio[61], 4), equals(0.0967)) expect_that(round(res$Ratio[62], 4), equals(0.0804)) expect_that(round(res$Ratio[63], 4), equals(0.0044)) expect_that(round(res$Ratio[64], 4), equals(0.0054)) expect_that(round(res$Ratio[65], 4), equals(0.006)) expect_that(round(res$Ratio[66], 4), equals(0.0801)) expect_that(round(res$Ratio[67], 4), equals(0.0493)) expect_that(round(res$Ratio[68], 4), equals(0.0046)) expect_that(round(res$Ratio[69], 4), equals(0.0099)) expect_that(round(res$Ratio[70], 4), equals(0.1376)) expect_that(round(res$Ratio[71], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(1)) expect_that(res$Type[5], equals(-2)) expect_that(res$Type[6], equals(-1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-2)) expect_that(res$Type[9], equals(1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(-2)) expect_that(res$Type[12], equals(1)) expect_that(res$Type[13], equals(-2)) expect_that(res$Type[14], equals(-1)) expect_that(res$Type[15], equals(-2)) expect_that(res$Type[16], equals(-2)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(1)) expect_that(res$Type[19], equals(-2)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(1)) expect_that(res$Type[22], equals(-1)) expect_that(res$Type[23], equals(-1)) expect_that(res$Type[24], equals(-1)) expect_that(res$Type[25], equals(1)) expect_that(res$Type[26], equals(-2)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(1)) expect_that(res$Type[29], equals(-1)) expect_that(res$Type[30], equals(1)) expect_that(res$Type[31], equals(-2)) expect_that(res$Type[32], equals(-1)) expect_that(res$Type[33], equals(1)) expect_that(res$Type[34], equals(-2)) expect_that(res$Type[35], equals(-1.8)) expect_that(res$Type[36], equals(-1)) expect_that(res$Type[37], equals(1)) expect_that(res$Type[38], equals(-1)) expect_that(res$Type[39], equals(-1)) expect_that(res$Type[40], equals(1)) expect_that(res$Type[41], equals(-2)) expect_that(res$Type[42], equals(-1)) expect_that(res$Type[43], equals(1)) expect_that(res$Type[44], equals(-1)) expect_that(res$Type[45], equals(-0.8)) expect_that(res$Type[46], equals(1)) expect_that(res$Type[47], equals(-2)) expect_that(res$Type[48], equals(-1.8)) expect_that(res$Type[49], equals(-1)) expect_that(res$Type[50], equals(1)) expect_that(res$Type[51], equals(1)) expect_that(res$Type[52], equals(-1.7)) expect_that(res$Type[53], equals(-1)) expect_that(res$Type[54], equals(1)) expect_that(res$Type[55], equals(-2)) expect_that(res$Type[56], equals(-1)) expect_that(res$Type[57], equals(1)) expect_that(res$Type[58], equals(-2)) expect_that(res$Type[59], equals(-1)) expect_that(res$Type[60], equals(-1)) expect_that(res$Type[61], equals(1)) expect_that(res$Type[62], equals(-1)) expect_that(res$Type[63], equals(-0.8)) expect_that(res$Type[64], equals(-2)) expect_that(res$Type[65], equals(-1.8)) expect_that(res$Type[66], equals(-1)) expect_that(res$Type[67], equals(-0.8)) expect_that(res$Type[68], equals(1)) expect_that(res$Type[69], equals(-2)) expect_that(res$Type[70], equals(-1)) expect_that(res$Type[71], equals(1)) # TEST 18 ------------------------------------------------------------------- # Test replacment of 'false' stutters. # 2 Back, 1 Forward, No interference. # Analyse dataframe. res <- calculateStutter( data = setA1, ref = ref4, back = 2, forward = 1, interference = 0, replace.val = c(-1.8, -0.8), by.val = c(-1.2, -0.2), debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.1216)) expect_that(round(res$Ratio[6], 4), equals(0.0142)) expect_that(round(res$Ratio[7], 4), equals(0.0768)) expect_that(round(res$Ratio[8], 4), equals(0.0961)) expect_that(round(res$Ratio[9], 4), equals(0.0417)) expect_that(round(res$Ratio[10], 4), equals(0.0782)) expect_that(round(res$Ratio[11], 4), equals(0.0086)) expect_that(round(res$Ratio[12], 4), equals(0.032)) expect_that(round(res$Ratio[13], 4), equals(0.0136)) expect_that(round(res$Ratio[14], 4), equals(0.0093)) expect_that(round(res$Ratio[15], 4), equals(0.1195)) expect_that(round(res$Ratio[16], 4), equals(0.0624)) expect_that(round(res$Ratio[17], 4), equals(0.0522)) expect_that(round(res$Ratio[18], 4), equals(0.0506)) expect_that(round(res$Ratio[19], 4), equals(0.0053)) expect_that(round(res$Ratio[20], 4), equals(0.0592)) expect_that(round(res$Ratio[21], 4), equals(0.0091)) expect_that(round(res$Ratio[22], 4), equals(0.0053)) expect_that(round(res$Ratio[23], 4), equals(0.0097)) expect_that(round(res$Ratio[24], 4), equals(0.0078)) expect_that(round(res$Ratio[25], 4), equals(0.0893)) expect_that(round(res$Ratio[26], 4), equals(0.0078)) expect_that(round(res$Ratio[27], 4), equals(0.0655)) expect_that(round(res$Ratio[28], 4), equals(0.0116)) expect_that(round(res$Ratio[29], 4), equals(0.0062)) expect_that(round(res$Ratio[30], 4), equals(0.1052)) expect_that(round(res$Ratio[31], 4), equals(0.0038)) expect_that(round(res$Ratio[32], 4), equals(0.015)) expect_that(round(res$Ratio[33], 4), equals(0.1832)) expect_that(round(res$Ratio[34], 4), equals(0.0044)) expect_that(round(res$Ratio[35], 4), equals(0.0054)) expect_that(round(res$Ratio[36], 4), equals(0.006)) expect_that(round(res$Ratio[37], 4), equals(0.0801)) expect_that(round(res$Ratio[38], 4), equals(0.0493)) expect_that(round(res$Ratio[39], 4), equals(0.0046)) expect_that(round(res$Ratio[40], 4), equals(0.0099)) expect_that(round(res$Ratio[41], 4), equals(0.1376)) expect_that(round(res$Ratio[42], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-2)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-0.2)) expect_that(res$Type[22], equals(1)) expect_that(res$Type[23], equals(-2)) expect_that(res$Type[24], equals(-1.2)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(1)) expect_that(res$Type[29], equals(-2)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(1)) expect_that(res$Type[32], equals(-2)) expect_that(res$Type[33], equals(-1)) expect_that(res$Type[34], equals(-0.2)) expect_that(res$Type[35], equals(-2)) expect_that(res$Type[36], equals(-1.2)) expect_that(res$Type[37], equals(-1)) expect_that(res$Type[38], equals(-0.2)) expect_that(res$Type[39], equals(1)) expect_that(res$Type[40], equals(-2)) expect_that(res$Type[41], equals(-1)) expect_that(res$Type[42], equals(1)) # TEST 19 ------------------------------------------------------------------- # Test single entries for homozygotes. # 2 Back, 1 Forward, No interference. refSingle <- ref4[!rownames(ref4) %in% c(2, 6), ] # Analyse dataframe. res <- calculateStutter( data = setA1, ref = refSingle, back = 2, forward = 1, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.1216)) expect_that(round(res$Ratio[6], 4), equals(0.0142)) expect_that(round(res$Ratio[7], 4), equals(0.0768)) expect_that(round(res$Ratio[8], 4), equals(0.0961)) expect_that(round(res$Ratio[9], 4), equals(0.0417)) expect_that(round(res$Ratio[10], 4), equals(0.0782)) expect_that(round(res$Ratio[11], 4), equals(0.0086)) expect_that(round(res$Ratio[12], 4), equals(0.032)) expect_that(round(res$Ratio[13], 4), equals(0.0136)) expect_that(round(res$Ratio[14], 4), equals(0.0093)) expect_that(round(res$Ratio[15], 4), equals(0.1195)) expect_that(round(res$Ratio[16], 4), equals(0.0624)) expect_that(round(res$Ratio[17], 4), equals(0.0522)) expect_that(round(res$Ratio[18], 4), equals(0.0506)) expect_that(round(res$Ratio[19], 4), equals(0.0053)) expect_that(round(res$Ratio[20], 4), equals(0.0592)) expect_that(round(res$Ratio[21], 4), equals(0.0091)) expect_that(round(res$Ratio[22], 4), equals(0.0053)) expect_that(round(res$Ratio[23], 4), equals(0.0097)) expect_that(round(res$Ratio[24], 4), equals(0.0078)) expect_that(round(res$Ratio[25], 4), equals(0.0893)) expect_that(round(res$Ratio[26], 4), equals(0.0078)) expect_that(round(res$Ratio[27], 4), equals(0.0655)) expect_that(round(res$Ratio[28], 4), equals(0.0116)) expect_that(round(res$Ratio[29], 4), equals(0.0062)) expect_that(round(res$Ratio[30], 4), equals(0.1052)) expect_that(round(res$Ratio[31], 4), equals(0.0038)) expect_that(round(res$Ratio[32], 4), equals(0.015)) expect_that(round(res$Ratio[33], 4), equals(0.1832)) expect_that(round(res$Ratio[34], 4), equals(0.0044)) expect_that(round(res$Ratio[35], 4), equals(0.0054)) expect_that(round(res$Ratio[36], 4), equals(0.006)) expect_that(round(res$Ratio[37], 4), equals(0.0801)) expect_that(round(res$Ratio[38], 4), equals(0.0493)) expect_that(round(res$Ratio[39], 4), equals(0.0046)) expect_that(round(res$Ratio[40], 4), equals(0.0099)) expect_that(round(res$Ratio[41], 4), equals(0.1376)) expect_that(round(res$Ratio[42], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-2)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-0.8)) expect_that(res$Type[22], equals(1)) expect_that(res$Type[23], equals(-2)) expect_that(res$Type[24], equals(-1.8)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(1)) expect_that(res$Type[29], equals(-2)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(1)) expect_that(res$Type[32], equals(-2)) expect_that(res$Type[33], equals(-1)) expect_that(res$Type[34], equals(-0.8)) expect_that(res$Type[35], equals(-2)) expect_that(res$Type[36], equals(-1.8)) expect_that(res$Type[37], equals(-1)) expect_that(res$Type[38], equals(-0.8)) expect_that(res$Type[39], equals(1)) expect_that(res$Type[40], equals(-2)) expect_that(res$Type[41], equals(-1)) expect_that(res$Type[42], equals(1)) # TEST 20 ------------------------------------------------------------------- # Test single entries for homozygotes. # 2 Back, 1 Forward, No interference. set4Missing <- set4[set4$Sample.Name != "07-A2.5", ] # Analyse dataframe. res <- calculateStutter( data = set4Missing, ref = ref4, back = 2, forward = 1, interference = 0, replace.val = NULL, by.val = NULL, debug = FALSE ) # write.table(x=res,"clipboard",sep="\t",row.names=FALSE,col.names=TRUE) # Check return class. expect_match(class(res), class(data.frame())) # Check that expected columns exist. expect_false(is.null(res$Marker)) expect_false(is.null(res$Allele)) expect_false(is.null(res$HeightA)) expect_false(is.null(res$Stutter)) expect_false(is.null(res$HeightS)) expect_false(is.null(res$Ratio)) expect_false(is.null(res$Type)) # Check result: Ratio. expect_that(round(res$Ratio[1], 4), equals(0.0035)) expect_that(round(res$Ratio[2], 4), equals(0.0264)) expect_that(round(res$Ratio[3], 4), equals(0.0062)) expect_that(round(res$Ratio[4], 4), equals(0.0889)) expect_that(round(res$Ratio[5], 4), equals(0.1216)) expect_that(round(res$Ratio[6], 4), equals(0.0142)) expect_that(round(res$Ratio[7], 4), equals(0.0768)) expect_that(round(res$Ratio[8], 4), equals(0.0961)) expect_that(round(res$Ratio[9], 4), equals(0.0417)) expect_that(round(res$Ratio[10], 4), equals(0.0782)) expect_that(round(res$Ratio[11], 4), equals(0.0086)) expect_that(round(res$Ratio[12], 4), equals(0.032)) expect_that(round(res$Ratio[13], 4), equals(0.0136)) expect_that(round(res$Ratio[14], 4), equals(0.0093)) expect_that(round(res$Ratio[15], 4), equals(0.1195)) expect_that(round(res$Ratio[16], 4), equals(0.0624)) expect_that(round(res$Ratio[17], 4), equals(0.0522)) expect_that(round(res$Ratio[18], 4), equals(0.0506)) expect_that(round(res$Ratio[19], 4), equals(0.0053)) expect_that(round(res$Ratio[20], 4), equals(0.0592)) expect_that(round(res$Ratio[21], 4), equals(0.0091)) expect_that(round(res$Ratio[22], 4), equals(0.0053)) expect_that(round(res$Ratio[23], 4), equals(0.0097)) expect_that(round(res$Ratio[24], 4), equals(0.0078)) expect_that(round(res$Ratio[25], 4), equals(0.0893)) expect_that(round(res$Ratio[26], 4), equals(0.0078)) expect_that(round(res$Ratio[27], 4), equals(0.0655)) expect_that(round(res$Ratio[28], 4), equals(0.0116)) expect_that(round(res$Ratio[29], 4), equals(0.0062)) expect_that(round(res$Ratio[30], 4), equals(0.1052)) expect_that(round(res$Ratio[31], 4), equals(0.0038)) expect_that(round(res$Ratio[32], 4), equals(0.015)) expect_that(round(res$Ratio[33], 4), equals(0.1832)) expect_that(round(res$Ratio[34], 4), equals(0.0044)) expect_that(round(res$Ratio[35], 4), equals(0.0054)) expect_that(round(res$Ratio[36], 4), equals(0.006)) expect_that(round(res$Ratio[37], 4), equals(0.0801)) expect_that(round(res$Ratio[38], 4), equals(0.0493)) expect_that(round(res$Ratio[39], 4), equals(0.0046)) expect_that(round(res$Ratio[40], 4), equals(0.0099)) expect_that(round(res$Ratio[41], 4), equals(0.1376)) expect_that(round(res$Ratio[42], 4), equals(0.007)) # Check result: Type. expect_that(res$Type[1], equals(-2)) expect_that(res$Type[2], equals(-1)) expect_that(res$Type[3], equals(-2)) expect_that(res$Type[4], equals(-1)) expect_that(res$Type[5], equals(-1)) expect_that(res$Type[6], equals(1)) expect_that(res$Type[7], equals(-1)) expect_that(res$Type[8], equals(-1)) expect_that(res$Type[9], equals(-1)) expect_that(res$Type[10], equals(-1)) expect_that(res$Type[11], equals(1)) expect_that(res$Type[12], equals(-1)) expect_that(res$Type[13], equals(1)) expect_that(res$Type[14], equals(-2)) expect_that(res$Type[15], equals(-1)) expect_that(res$Type[16], equals(1)) expect_that(res$Type[17], equals(-1)) expect_that(res$Type[18], equals(-1)) expect_that(res$Type[19], equals(1)) expect_that(res$Type[20], equals(-1)) expect_that(res$Type[21], equals(-0.8)) expect_that(res$Type[22], equals(1)) expect_that(res$Type[23], equals(-2)) expect_that(res$Type[24], equals(-1.8)) expect_that(res$Type[25], equals(-1)) expect_that(res$Type[26], equals(1)) expect_that(res$Type[27], equals(-1)) expect_that(res$Type[28], equals(1)) expect_that(res$Type[29], equals(-2)) expect_that(res$Type[30], equals(-1)) expect_that(res$Type[31], equals(1)) expect_that(res$Type[32], equals(-2)) expect_that(res$Type[33], equals(-1)) expect_that(res$Type[34], equals(-0.8)) expect_that(res$Type[35], equals(-2)) expect_that(res$Type[36], equals(-1.8)) expect_that(res$Type[37], equals(-1)) expect_that(res$Type[38], equals(-0.8)) expect_that(res$Type[39], equals(1)) expect_that(res$Type[40], equals(-2)) expect_that(res$Type[41], equals(-1)) expect_that(res$Type[42], equals(1)) })