tests/testthat/test_peakPantheR_loadAnnotationParamsCSV.R
In phenomecentre/peakPantheR: Peak Picking and Annotation of High Resolution Experiments
context('peakPantheR_loadAnnotationParamsCSV()')
## Test the generation of a new object by reading parameters from CSV (simple: Spl, advanced: Adv)
# Also test prepare_basic_target_parameters() and prepare_advanced_target_parameters()
## Input data
input_CSV_adv <- data.frame(matrix(nrow=2,ncol=21,dimnames=list(c(), c('cpdID', 'cpdName', 'X', 'ROI_rt', 'ROI_mz','ROI_rtMin', 'ROI_rtMax', 'ROI_mzMin', 'ROI_mzMax', 'X', 'uROI_rtMin', 'uROI_rtMax', 'uROI_mzMin', 'uROI_mzMax', 'uROI_rt', 'uROI_mz', 'X', 'FIR_rtMin', 'FIR_rtMax', 'FIR_mzMin', 'FIR_mzMax'))))
input_CSV_adv[1,] <- c('ID-1', 'Cpd 1', '|', 1., 2., 3., 4., 5., 6., '|', 7., 8., 9., 10., 11., 12., '|', 13., 14., 15., 16.)
input_CSV_adv[2,] <- c('ID-2', 'Cpd 2', '|', 17., 18., 19., 20., 21., 22., '|', 23., 24., 25., 26., 27., 28., '|', 29., 30., 31., 32.)
input_CSV_adv[,-c(1,2,3,10,17)] <- sapply(input_CSV_adv[,-c(1,2,3,10,17)], as.numeric)
input_CSV_spl <- input_CSV_adv[, c('cpdID', 'cpdName', 'ROI_rtMin', 'ROI_rt', 'ROI_rtMax', 'ROI_mzMin', 'ROI_mz', 'ROI_mzMax')]
colnames(input_CSV_spl) <- c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax")
## Expected result
# targetFeatTable
input_targetFeatTable_adv <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=FALSE)
input_targetFeatTable_adv[1,] <- c("ID-1", "Cpd 1", 3., 1., 4., 5., 2., 6.)
input_targetFeatTable_adv[2,] <- c("ID-2", "Cpd 2", 19., 17., 20., 21., 18., 22.)
input_targetFeatTable_adv[,c(3:8)] <- sapply(input_targetFeatTable_adv[,c(3:8)], as.numeric)
input_targetFeatTable_spl <- input_targetFeatTable_adv
# uROI
input_uROI_adv <- data.frame(matrix(vector(), 2, 6, dimnames=list(c(), c("rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=FALSE)
input_uROI_adv[1,] <- c( 7., 11. , 8., 9., 12., 10.)
input_uROI_adv[2,] <- c(23., 27., 24., 25., 28., 26.)
# FIR
input_FIR_adv <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(), c("rtMin", "rtMax", "mzMin", "mzMax"))), stringsAsFactors=FALSE)
input_FIR_adv[1,] <- c(13., 14., 15., 16.)
input_FIR_adv[2,] <- c(29., 30., 31., 32.)
# object
input_annotation_adv <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable_adv,
uROI = input_uROI_adv,
FIR = input_FIR_adv,
uROIExist = TRUE)
input_annotation_spl <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable_spl)
test_that('Spl - default with ROI, verbose, no verbose', {
# temporary file
savePath1 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
# save csv
utils::write.csv(input_CSV_spl, file=savePath1, row.names=FALSE)
# expected
expected_annotation <- input_annotation_spl
expected_message <- c("New peakPantheRAnnotation object initialised for 2 compounds\n")
# results (output, warnings and messages)
result_load1 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath1, verbose=TRUE))
# Check result
expect_equal(result_load1$result, expected_annotation)
# Check result messages
expect_equal(length(result_load1$messages), 1)
expect_equal(result_load1$messages, expected_message)
## no verbose
result_load2 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath1, verbose=FALSE))
expect_equal(length(result_load2$messages), 0)
})
test_that('Adv - default with ROI, uROI, FIR, uROIExist=TRUE, verbose, no verbose', {
# temporary file
savePath2 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
# save csv
utils::write.csv(input_CSV_adv, file=savePath2, row.names=FALSE)
# expected
expected_annotation <- input_annotation_adv
expected_message <- c("uROIExist set to TRUE\n", "New peakPantheRAnnotation object initialised for 2 compounds\n")
# results (output, warnings and messages)
result_load1 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath2, verbose=TRUE))
# Check result
expect_equal(result_load1$result, expected_annotation)
# Check result messages
expect_equal(length(result_load1$messages), 2)
expect_equal(result_load1$messages, expected_message)
## no verbose
result_load2 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath2, verbose=FALSE))
expect_equal(length(result_load2$messages), 0)
})
test_that('Adv - ROI with NA, uROI with NA, FIR with NA, uROIExist=FALSE, verbose, no verbose', {
# NA in ROI_rt mz are allowed, NA in uROI set uROIExist=FALSE, NA in FIR is allowed
# temporary file
savePath3 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
# save csv
tmp_CSV <- input_CSV_adv
tmp_CSV$ROI_rt <- c(as.numeric(NA), 17.)
tmp_CSV$ROI_mz <- c(2, as.numeric(NA))
tmp_CSV$uROI_rtMin <- c(7., as.numeric(NA))
tmp_CSV$FIR_mzMax <- c(as.numeric(NA), as.numeric(NA))
utils::write.csv(tmp_CSV, file=savePath3, row.names=FALSE)
# expected
tmp_targetFeatTable <- input_targetFeatTable_adv
tmp_targetFeatTable$rt <- c(as.numeric(NA), 17.)
tmp_targetFeatTable$mz <- c(2, as.numeric(NA))
tmp_uROI <- input_uROI_adv
tmp_uROI$rtMin <- c(7., as.numeric(NA))
tmp_FIR <- input_FIR_adv
tmp_FIR$mzMax <- c(as.numeric(NA), as.numeric(NA))
expected_annotation <- peakPantheRAnnotation(targetFeatTable=tmp_targetFeatTable, uROI=tmp_uROI, FIR=tmp_FIR, uROIExist=FALSE)
expected_message <- c("NA in uROI, uROIExist is set to FALSE\n", "New peakPantheRAnnotation object initialised for 2 compounds\n")
# results (output, warnings and messages)
result_load1 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath3, verbose=TRUE))
# Check result
expect_equal(result_load1$result, expected_annotation)
# Check result messages
expect_equal(length(result_load1$messages), 2)
expect_equal(result_load1$messages, expected_message)
## no verbose
result_load2 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath3, verbose=FALSE))
expect_equal(length(result_load2$messages), 0)
})
test_that('raise errors - peakPantheR_loadAnnotationParamsCSV', {
# file doesn't exist
noFile <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
msg1 <- paste('specified "CSVParamPath" does not exist', sep='')
expect_error(peakPantheR_loadAnnotationParamsCSV(noFile, verbose=TRUE), msg1, fixed=TRUE)
})
test_that('prepare_basic_target_parameters', {
# expected
expected_targetFeatTable <- input_targetFeatTable_spl
expected_uROI <- data.frame(rtMin=numeric(), rt=numeric(), rtMax=numeric(), mzMin=numeric(), mz=numeric(), mzMax=numeric(), stringsAsFactors=FALSE)
expected_FIR <- data.frame(rtMin=numeric(), rtMax=numeric(), mzMin=numeric(), mzMax=numeric(), stringsAsFactors=FALSE)
expected_uROIExist <- FALSE
# results (output, warnings and messages)
result_prepare1 <- evaluate_promise(prepare_basic_target_parameters(input_CSV_spl))
# Check result
expect_equal(result_prepare1$result$targetFeatTable, expected_targetFeatTable)
expect_equal(result_prepare1$result$uROI, expected_uROI)
expect_equal(result_prepare1$result$FIR, expected_FIR)
expect_equal(result_prepare1$result$uROIExist, expected_uROIExist)
# Check result messages
expect_equal(length(result_prepare1$messages), 0)
})
test_that('raise errors - prepare_basic_target_parameters', {
# expected columns are missing
wrongCol_spl <- data.frame(matrix(nrow=2,ncol=2,dimnames=list(c(), c('wrongCol','notAColumn'))))
msg2 <- paste('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"')
expect_error(prepare_basic_target_parameters(wrongCol_spl), msg2, fixed=TRUE)
# ROI rtMin > rtMax
wrongROIrt_spl <- input_CSV_spl
wrongROIrt_spl$rtMin <- c(5, 19)
msg3 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_basic_target_parameters(wrongROIrt_spl), msg3, fixed=TRUE)
# ROI mzMin > mzMax
wrongROImz_spl <- input_CSV_spl
wrongROImz_spl$mzMin <- c(5, 23)
msg4 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_basic_target_parameters(wrongROImz_spl), msg4, fixed=TRUE)
# ROI rtMin is NA
wrongROIrtMin <- input_CSV_spl
wrongROIrtMin$rtMin <- c(NA, 19)
msg4 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROIrtMin), msg4, fixed=TRUE)
# ROI rtMax is NA
wrongROIrtMax <- input_CSV_spl
wrongROIrtMax$rtMax <- c(4, NA)
msg5 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROIrtMax), msg5, fixed=TRUE)
# ROI mzMin is NA
wrongROImzMin <- input_CSV_spl
wrongROImzMin$mzMin <- c(NA, 21)
msg6 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROImzMin), msg6, fixed=TRUE)
# ROI mzMax is NA
wrongROImzMax <- input_CSV_spl
wrongROImzMax$mzMax <- c(6, NA)
msg7 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROImzMax), msg7, fixed=TRUE)
})
test_that('prepare_advanced_target_parameters', {
# expected
expected_targetFeatTable <- input_targetFeatTable_adv
expected_uROI <- input_uROI_adv
expected_FIR <- input_FIR_adv
expected_uROIExist <- TRUE
expected_message <- c("uROIExist set to TRUE\n")
# results (output, warnings and messages)
result_prepare1 <- evaluate_promise(prepare_advanced_target_parameters(input_CSV_adv, verbose=TRUE))
# Check result
expect_equal(result_prepare1$result$targetFeatTable, expected_targetFeatTable)
expect_equal(result_prepare1$result$uROI, expected_uROI)
expect_equal(result_prepare1$result$FIR, expected_FIR)
expect_equal(result_prepare1$result$uROIExist, expected_uROIExist)
# Check result messages
expect_equal(length(result_prepare1$messages), 1)
expect_equal(result_prepare1$messages, expected_message)
})
test_that('raise errors - prepare_advanced_target_parameters', {
# expected columns are missing
wrongCol_adv <- data.frame(matrix(nrow=2,ncol=2,dimnames=list(c(), c('wrongCol','notAColumn'))))
msg5 <- paste('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "ROI_rt", "ROI_mz", "ROI_rtMin", "ROI_rtMax", "ROI_mzMin", "ROI_mzMax", "uROI_rtMin", "uROI_rtMax", "uROI_mzMin", "uROI_mzMax", "uROI_rt", "uROI_mz", "FIR_rtMin", "FIR_rtMax", "FIR_mzMin", "FIR_mzMax"')
expect_error(prepare_advanced_target_parameters(wrongCol_adv, verbose=TRUE), msg5, fixed=TRUE)
# ROI rtMin > rtMax
wrongROIrt_adv <- input_CSV_adv
wrongROIrt_adv$ROI_rtMin <- c(5, 19)
msg6 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongROIrt_adv, verbose=FALSE), msg6, fixed=TRUE)
# ROI mzMin > mzMax
wrongROImz_adv <- input_CSV_adv
wrongROImz_adv$ROI_mzMin <- c(5, 23)
msg7 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongROImz_adv, verbose=FALSE), msg7, fixed=TRUE)
# ROI rtMin is NA
wrongROIrtMin <- input_CSV_adv
wrongROIrtMin$ROI_rtMin <- c(NA, 19)
msg10 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROIrtMin, verbose=FALSE), msg10, fixed=TRUE)
# ROI rtMax is NA
wrongROIrtMax <- input_CSV_adv
wrongROIrtMax$ROI_rtMax <- c(4, NA)
msg11 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROIrtMax, verbose=FALSE), msg11, fixed=TRUE)
# ROI mzMin is NA
wrongROImzMin <- input_CSV_adv
wrongROImzMin$ROI_mzMin <- c(NA, 21)
msg12 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROImzMin, verbose=FALSE), msg12, fixed=TRUE)
# ROI mzMax is NA
wrongROImzMax <- input_CSV_adv
wrongROImzMax$ROI_mzMax <- c(6, NA)
msg13 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROImzMax, verbose=FALSE), msg13, fixed=TRUE)
# uROI rtMin > rtMax
wrongUROIrt <- input_CSV_adv
wrongUROIrt$uROI_rtMin <- c(7, 25)
msg8 <- paste('Check uROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongUROIrt, verbose=FALSE), msg8, fixed=TRUE)
# uROI mzMin < mzMax
wrongUROImz <- input_CSV_adv
wrongUROImz$uROI_mzMin <- c(12, 25)
msg9 <- paste('Check uROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongUROImz, verbose=FALSE), msg9, fixed=TRUE)
})
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context('peakPantheR_loadAnnotationParamsCSV()')
## Test the generation of a new object by reading parameters from CSV (simple: Spl, advanced: Adv)
# Also test prepare_basic_target_parameters() and prepare_advanced_target_parameters()
## Input data
input_CSV_adv <- data.frame(matrix(nrow=2,ncol=21,dimnames=list(c(), c('cpdID', 'cpdName', 'X', 'ROI_rt', 'ROI_mz','ROI_rtMin', 'ROI_rtMax', 'ROI_mzMin', 'ROI_mzMax', 'X', 'uROI_rtMin', 'uROI_rtMax', 'uROI_mzMin', 'uROI_mzMax', 'uROI_rt', 'uROI_mz', 'X', 'FIR_rtMin', 'FIR_rtMax', 'FIR_mzMin', 'FIR_mzMax'))))
input_CSV_adv[1,] <- c('ID-1', 'Cpd 1', '|', 1., 2., 3., 4., 5., 6., '|', 7., 8., 9., 10., 11., 12., '|', 13., 14., 15., 16.)
input_CSV_adv[2,] <- c('ID-2', 'Cpd 2', '|', 17., 18., 19., 20., 21., 22., '|', 23., 24., 25., 26., 27., 28., '|', 29., 30., 31., 32.)
input_CSV_adv[,-c(1,2,3,10,17)] <- sapply(input_CSV_adv[,-c(1,2,3,10,17)], as.numeric)
input_CSV_spl <- input_CSV_adv[, c('cpdID', 'cpdName', 'ROI_rtMin', 'ROI_rt', 'ROI_rtMax', 'ROI_mzMin', 'ROI_mz', 'ROI_mzMax')]
colnames(input_CSV_spl) <- c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax")
## Expected result
# targetFeatTable
input_targetFeatTable_adv <- data.frame(matrix(vector(), 2, 8, dimnames=list(c(), c("cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=FALSE)
input_targetFeatTable_adv[1,] <- c("ID-1", "Cpd 1", 3., 1., 4., 5., 2., 6.)
input_targetFeatTable_adv[2,] <- c("ID-2", "Cpd 2", 19., 17., 20., 21., 18., 22.)
input_targetFeatTable_adv[,c(3:8)] <- sapply(input_targetFeatTable_adv[,c(3:8)], as.numeric)
input_targetFeatTable_spl <- input_targetFeatTable_adv
# uROI
input_uROI_adv <- data.frame(matrix(vector(), 2, 6, dimnames=list(c(), c("rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"))), stringsAsFactors=FALSE)
input_uROI_adv[1,] <- c( 7., 11. , 8., 9., 12., 10.)
input_uROI_adv[2,] <- c(23., 27., 24., 25., 28., 26.)
# FIR
input_FIR_adv <- data.frame(matrix(vector(), 2, 4, dimnames=list(c(), c("rtMin", "rtMax", "mzMin", "mzMax"))), stringsAsFactors=FALSE)
input_FIR_adv[1,] <- c(13., 14., 15., 16.)
input_FIR_adv[2,] <- c(29., 30., 31., 32.)
# object
input_annotation_adv <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable_adv,
uROI = input_uROI_adv,
FIR = input_FIR_adv,
uROIExist = TRUE)
input_annotation_spl <- peakPantheRAnnotation(targetFeatTable = input_targetFeatTable_spl)
test_that('Spl - default with ROI, verbose, no verbose', {
# temporary file
savePath1 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
# save csv
utils::write.csv(input_CSV_spl, file=savePath1, row.names=FALSE)
# expected
expected_annotation <- input_annotation_spl
expected_message <- c("New peakPantheRAnnotation object initialised for 2 compounds\n")
# results (output, warnings and messages)
result_load1 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath1, verbose=TRUE))
# Check result
expect_equal(result_load1$result, expected_annotation)
# Check result messages
expect_equal(length(result_load1$messages), 1)
expect_equal(result_load1$messages, expected_message)
## no verbose
result_load2 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath1, verbose=FALSE))
expect_equal(length(result_load2$messages), 0)
})
test_that('Adv - default with ROI, uROI, FIR, uROIExist=TRUE, verbose, no verbose', {
# temporary file
savePath2 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
# save csv
utils::write.csv(input_CSV_adv, file=savePath2, row.names=FALSE)
# expected
expected_annotation <- input_annotation_adv
expected_message <- c("uROIExist set to TRUE\n", "New peakPantheRAnnotation object initialised for 2 compounds\n")
# results (output, warnings and messages)
result_load1 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath2, verbose=TRUE))
# Check result
expect_equal(result_load1$result, expected_annotation)
# Check result messages
expect_equal(length(result_load1$messages), 2)
expect_equal(result_load1$messages, expected_message)
## no verbose
result_load2 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath2, verbose=FALSE))
expect_equal(length(result_load2$messages), 0)
})
test_that('Adv - ROI with NA, uROI with NA, FIR with NA, uROIExist=FALSE, verbose, no verbose', {
# NA in ROI_rt mz are allowed, NA in uROI set uROIExist=FALSE, NA in FIR is allowed
# temporary file
savePath3 <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
# save csv
tmp_CSV <- input_CSV_adv
tmp_CSV$ROI_rt <- c(as.numeric(NA), 17.)
tmp_CSV$ROI_mz <- c(2, as.numeric(NA))
tmp_CSV$uROI_rtMin <- c(7., as.numeric(NA))
tmp_CSV$FIR_mzMax <- c(as.numeric(NA), as.numeric(NA))
utils::write.csv(tmp_CSV, file=savePath3, row.names=FALSE)
# expected
tmp_targetFeatTable <- input_targetFeatTable_adv
tmp_targetFeatTable$rt <- c(as.numeric(NA), 17.)
tmp_targetFeatTable$mz <- c(2, as.numeric(NA))
tmp_uROI <- input_uROI_adv
tmp_uROI$rtMin <- c(7., as.numeric(NA))
tmp_FIR <- input_FIR_adv
tmp_FIR$mzMax <- c(as.numeric(NA), as.numeric(NA))
expected_annotation <- peakPantheRAnnotation(targetFeatTable=tmp_targetFeatTable, uROI=tmp_uROI, FIR=tmp_FIR, uROIExist=FALSE)
expected_message <- c("NA in uROI, uROIExist is set to FALSE\n", "New peakPantheRAnnotation object initialised for 2 compounds\n")
# results (output, warnings and messages)
result_load1 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath3, verbose=TRUE))
# Check result
expect_equal(result_load1$result, expected_annotation)
# Check result messages
expect_equal(length(result_load1$messages), 2)
expect_equal(result_load1$messages, expected_message)
## no verbose
result_load2 <- evaluate_promise(peakPantheR_loadAnnotationParamsCSV(savePath3, verbose=FALSE))
expect_equal(length(result_load2$messages), 0)
})
test_that('raise errors - peakPantheR_loadAnnotationParamsCSV', {
# file doesn't exist
noFile <- tempfile(pattern="file", tmpdir=tempdir(), fileext='.csv')
msg1 <- paste('specified "CSVParamPath" does not exist', sep='')
expect_error(peakPantheR_loadAnnotationParamsCSV(noFile, verbose=TRUE), msg1, fixed=TRUE)
})
test_that('prepare_basic_target_parameters', {
# expected
expected_targetFeatTable <- input_targetFeatTable_spl
expected_uROI <- data.frame(rtMin=numeric(), rt=numeric(), rtMax=numeric(), mzMin=numeric(), mz=numeric(), mzMax=numeric(), stringsAsFactors=FALSE)
expected_FIR <- data.frame(rtMin=numeric(), rtMax=numeric(), mzMin=numeric(), mzMax=numeric(), stringsAsFactors=FALSE)
expected_uROIExist <- FALSE
# results (output, warnings and messages)
result_prepare1 <- evaluate_promise(prepare_basic_target_parameters(input_CSV_spl))
# Check result
expect_equal(result_prepare1$result$targetFeatTable, expected_targetFeatTable)
expect_equal(result_prepare1$result$uROI, expected_uROI)
expect_equal(result_prepare1$result$FIR, expected_FIR)
expect_equal(result_prepare1$result$uROIExist, expected_uROIExist)
# Check result messages
expect_equal(length(result_prepare1$messages), 0)
})
test_that('raise errors - prepare_basic_target_parameters', {
# expected columns are missing
wrongCol_spl <- data.frame(matrix(nrow=2,ncol=2,dimnames=list(c(), c('wrongCol','notAColumn'))))
msg2 <- paste('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "rtMin", "rt", "rtMax", "mzMin", "mz", "mzMax"')
expect_error(prepare_basic_target_parameters(wrongCol_spl), msg2, fixed=TRUE)
# ROI rtMin > rtMax
wrongROIrt_spl <- input_CSV_spl
wrongROIrt_spl$rtMin <- c(5, 19)
msg3 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_basic_target_parameters(wrongROIrt_spl), msg3, fixed=TRUE)
# ROI mzMin > mzMax
wrongROImz_spl <- input_CSV_spl
wrongROImz_spl$mzMin <- c(5, 23)
msg4 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_basic_target_parameters(wrongROImz_spl), msg4, fixed=TRUE)
# ROI rtMin is NA
wrongROIrtMin <- input_CSV_spl
wrongROIrtMin$rtMin <- c(NA, 19)
msg4 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROIrtMin), msg4, fixed=TRUE)
# ROI rtMax is NA
wrongROIrtMax <- input_CSV_spl
wrongROIrtMax$rtMax <- c(4, NA)
msg5 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROIrtMax), msg5, fixed=TRUE)
# ROI mzMin is NA
wrongROImzMin <- input_CSV_spl
wrongROImzMin$mzMin <- c(NA, 21)
msg6 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROImzMin), msg6, fixed=TRUE)
# ROI mzMax is NA
wrongROImzMax <- input_CSV_spl
wrongROImzMax$mzMax <- c(6, NA)
msg7 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_basic_target_parameters(wrongROImzMax), msg7, fixed=TRUE)
})
test_that('prepare_advanced_target_parameters', {
# expected
expected_targetFeatTable <- input_targetFeatTable_adv
expected_uROI <- input_uROI_adv
expected_FIR <- input_FIR_adv
expected_uROIExist <- TRUE
expected_message <- c("uROIExist set to TRUE\n")
# results (output, warnings and messages)
result_prepare1 <- evaluate_promise(prepare_advanced_target_parameters(input_CSV_adv, verbose=TRUE))
# Check result
expect_equal(result_prepare1$result$targetFeatTable, expected_targetFeatTable)
expect_equal(result_prepare1$result$uROI, expected_uROI)
expect_equal(result_prepare1$result$FIR, expected_FIR)
expect_equal(result_prepare1$result$uROIExist, expected_uROIExist)
# Check result messages
expect_equal(length(result_prepare1$messages), 1)
expect_equal(result_prepare1$messages, expected_message)
})
test_that('raise errors - prepare_advanced_target_parameters', {
# expected columns are missing
wrongCol_adv <- data.frame(matrix(nrow=2,ncol=2,dimnames=list(c(), c('wrongCol','notAColumn'))))
msg5 <- paste('Columns in "CSVParamPath" must be: "cpdID", "cpdName", "ROI_rt", "ROI_mz", "ROI_rtMin", "ROI_rtMax", "ROI_mzMin", "ROI_mzMax", "uROI_rtMin", "uROI_rtMax", "uROI_mzMin", "uROI_mzMax", "uROI_rt", "uROI_mz", "FIR_rtMin", "FIR_rtMax", "FIR_mzMin", "FIR_mzMax"')
expect_error(prepare_advanced_target_parameters(wrongCol_adv, verbose=TRUE), msg5, fixed=TRUE)
# ROI rtMin > rtMax
wrongROIrt_adv <- input_CSV_adv
wrongROIrt_adv$ROI_rtMin <- c(5, 19)
msg6 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongROIrt_adv, verbose=FALSE), msg6, fixed=TRUE)
# ROI mzMin > mzMax
wrongROImz_adv <- input_CSV_adv
wrongROImz_adv$ROI_mzMin <- c(5, 23)
msg7 <- paste('Check ROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongROImz_adv, verbose=FALSE), msg7, fixed=TRUE)
# ROI rtMin is NA
wrongROIrtMin <- input_CSV_adv
wrongROIrtMin$ROI_rtMin <- c(NA, 19)
msg10 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROIrtMin, verbose=FALSE), msg10, fixed=TRUE)
# ROI rtMax is NA
wrongROIrtMax <- input_CSV_adv
wrongROIrtMax$ROI_rtMax <- c(4, NA)
msg11 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROIrtMax, verbose=FALSE), msg11, fixed=TRUE)
# ROI mzMin is NA
wrongROImzMin <- input_CSV_adv
wrongROImzMin$ROI_mzMin <- c(NA, 21)
msg12 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROImzMin, verbose=FALSE), msg12, fixed=TRUE)
# ROI mzMax is NA
wrongROImzMax <- input_CSV_adv
wrongROImzMax$ROI_mzMax <- c(6, NA)
msg13 <- paste('Check ROI values: "ROI$rtMin", "ROI$rtMax", "ROI$mzMin" and "ROI$mzMax" cannot be NA')
expect_error(prepare_advanced_target_parameters(wrongROImzMax, verbose=FALSE), msg13, fixed=TRUE)
# uROI rtMin > rtMax
wrongUROIrt <- input_CSV_adv
wrongUROIrt$uROI_rtMin <- c(7, 25)
msg8 <- paste('Check uROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongUROIrt, verbose=FALSE), msg8, fixed=TRUE)
# uROI mzMin < mzMax
wrongUROImz <- input_CSV_adv
wrongUROImz$uROI_mzMin <- c(12, 25)
msg9 <- paste('Check uROI values: "rtMin" < "rtMax" and "mzMin" < "mzMax"')
expect_error(prepare_advanced_target_parameters(wrongUROImz, verbose=FALSE), msg9, fixed=TRUE)
})
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