testthat::context("Test Peak detection")
test_PeakList<-function(){
## error
testthat::expect_error(PeakList(NULL))
library(ptairData)
filePath <- system.file("extdata/exhaledAir/ind1", "ind1-1.h5",
package = "ptairData")
file <- readRaw(filePath,mzCalibRef = c(21.022,59.049))
peakList <- PeakList(file, mzNominal = 21,fctFit = "averagePeak")
peakList2 <- PeakList(file, mzNominal = 21,fctFit = "sech2")
peakList3 <- PeakList(file, mzNominal = 21,fctFit = "asymGauss")
## find isotope of primary ion (always present)
testthat::expect_true(dim(peakList$peak)[1] >= 1)
testthat::expect_true(dim(peakList2$peak)[1] >= 1)
testthat::expect_true(dim(peakList3$peak)[1] >= 1)
peakList <- PeakList(file, mzNominal = 63)
testthat::expect_true(nrow(peakList$peak) == 3)
}
test_peakSet<-function(){
library(ptairData)
dir <- system.file("extdata/mycobacteria", package = "ptairData")
dirSet <- createPtrSet(dir = dir, setName = "test",
mzCalibRef = c(21.022,59.049))
ListFiles <- names(getTimeInfo(dirSet)$TIC)
peakLists <- detectPeak(dirSet, smoothPenalty = 0,
resolutionRange = c(3000,5000,9000),
mzNominal = c(21,59))
# type,
testthat::expect_is(peakLists,'ptrSet')
testthat::expect_true(all(sapply(getPeakList(peakLists),function(x)
nrow(Biobase::exprs(x))>=2)))
}
testthat::test_that("PeakList() work", test_PeakList())
testthat::test_that("peakSet() work", test_peakSet())
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