inst/unitTests/test_mzid.R

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

test_mzid <- function() {
    library("mzID")
    file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")
    x <- openIDfile(file)
    validObject(x)
    y <- mzID(file)
    fy <- flatten(y)
    s <- score(x)
    checkTrue(identical(s$X.Tandem.hyperscore, fy$"x\\!tandem:hyperscore"))
    checkTrue(identical(s$X.Tandem.expect, fy$"x\\!tandem:expect"))
    p <- psms(x)
    checkTrue(identical(as.character(p$spectrumID), fy$spectrumid))
    checkTrue(identical(as.character(p$post), fy$post))
    checkTrue(identical(as.character(p$sequence), fy$pepseq))
    checkTrue(identical(as.character(p$DatabaseAccess), fy$accession))
}