tests/testthat/test_200_lcms_annotation.R

In pkrog/biodb: biodb, a library and a development framework for connecting to chemical and biological databases

test_annotateWithMassCsvFileDb <- function(biodb) {
    mzdf <- data.frame(mz=c(282.083871, 283.0623, 346.0546, 821.3964),
                       rt=c(334, 872, 536, 740))
    lcmsdb <- system.file("extdata", "massbank_extract_lcms_1.tsv",
                          package="biodb")
    massbank <- biodb$getFactory()$createConn('mass.csv.file', url=lcmsdb)
    massbank$addField('ms.level', 1)
    massbank$addField('chrom.rt.unit', 's')
    x <- massbank$searchMsPeaks(mzdf, mz.tol=1e-3, prefix='mydb.',
                                fields=c('accession', 'name', 'formula',
                                         'chebi.id'))
    testthat::expect_is(x, 'data.frame')
    testthat::expect_true(nrow(x) >= nrow(mzdf))
    chromColIds <- c('TOSOH TSKgel ODS-100V  5um Part no. 21456')
    fields <- c('accession', 'name', 'formula', 'chebi.id', 'chrom.rt',
                'chrom.col.id')
    x <- massbank$searchMsPeaks(mzdf, mz.tol=1e-3, fields=fields,
                                prefix='mydb.', chrom.col.ids=chromColIds,
                                rt.unit='s', rt.tol=10, match.rt=TRUE)
    testthat::expect_is(x, 'data.frame')
    testthat::expect_true(nrow(x) >= nrow(mzdf))
}

# Instantiate Biodb
biodb <- biodb::createBiodbTestInstance()

# Set context
biodb::testContext("Test LCMS annotation.")

# Run tests
biodb::testThat("We can annotate using mass CSV file db.",
                test_annotateWithMassCsvFileDb, biodb=biodb)

# Terminate Biodb
biodb$terminate()