tests/testthat.R

In rformassspectrometry/Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

library(testthat)
library(Chromatograms)

### Test ChrombackendMzR
# fetch files
MRM_file <- system.file("proteomics", "MRM-standmix-5.mzML.gz",
                        package = "msdata")
be_empty <- ChromBackendMzR()
be <- backendInitialize(be_empty, files = MRM_file, BPPARAM = SerialParam())

test_suite <- system.file("test_backends", "test_ChromBackend",
                          package = "Chromatograms")
test_dir(test_suite, stop_on_failure = TRUE) #pass

be_mzr <- be
c_mzr <- Chromatograms(be)

### Test ChrombackendMemory
cdata <- data.frame(msLevel = c(1L, 1L, 1L),
                    mz = c(112.2, 123.3, 134.4),
                    chromIndex = c(1L, 2L, 3L))
pdata <- list(
    data.frame(rtime = c(12.4, 12.8, 13.2, 14.6),
               intensity = c(123.3, 153.6, 2354.3, 243.4)),
    data.frame(rtime = c(45.1, 46.2),
               intensity = c(100, 80.1)),
    data.frame(rtime = c(12.4, 12.8, 13.2, 14.6),
               intensity = c(123.3, 153.6, 2354.3, 243.4))
)

be_empty <- new("ChromBackendMemory")
be_cd <- backendInitialize(be_empty, chromData = cdata)
be <- backendInitialize(be_empty, chromData = cdata, peaksData = pdata)
test_dir(test_suite, stop_on_failure = TRUE)

c_empty <- Chromatograms()
c_full <- Chromatograms(be)

test_check("Chromatograms")