inst/unitTests/test_header.R

In sneumann/mzR: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)

test_header_all <- function() {
    ## Check that the header call returns the same columns irrespectively of the
    ## backend. Issue #238
    file <- system.file('cdf/ko15.CDF', package = "msdata")
    cdf <- openMSfile(file, backend="netCDF")
    header_cdf <- header(cdf)
    close(cdf)

    file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML", package = "msdata")
    mzxml <- openMSfile(file, backend="pwiz")
    header_pwiz <- header(mzxml)
    close(mzxml)

    neededCdfHeaders <- c("seqNum", "acquisitionNum", "msLevel", "polarity", "peaksCount",  
                          "totIonCurrent", "retentionTime", "basePeakMZ", "basePeakIntensity",  
                          "collisionEnergy", "ionisationEnergy", "lowMZ", "highMZ", "precursorScanNum",  
                          "precursorMZ", "precursorCharge", "precursorIntensity", "mergedScan",  
                          "mergedResultScanNum", "mergedResultStartScanNum", "mergedResultEndScanNum",  
                          "injectionTime", "filterString", "spectrumId", "centroided",  
                          "ionMobilityDriftTime", "isolationWindowTargetMZ", "isolationWindowLowerOffset",  
                          "isolationWindowUpperOffset", "scanWindowLowerLimit", "scanWindowUpperLimit" )
    
    checkTrue( all(neededCdfHeaders %in% colnames(header_cdf)) )
    checkTrue( all(neededCdfHeaders %in% colnames(header_pwiz)) )
}