tests/testthat/test-fragmentIon.R

In protViz/protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics

#R

context("fragmentIons")

test_that("HTLNQIDSVK", {
    m <- fragmentIon('HTLNQIDSVK')[[1]]

    b_assumed <- c(138.0662, 239.1139, 352.1979, 466.2409, 594.2994, 
        707.3835, 822.4104, 909.4425, 1008.5109, 1136.6058)

    lapply(1:length(m$b), function(i){
        expect_equal(m$b[i], b_assumed[i], tolerance = 1e-03)
    })


    expect_equal(m$y[5], 561.3242, tolerance=1e-03)

})


test_that("KINHSFLR", {
     peptide.AA <- "KINHSFLR";
     peptide.AA.weights <- c(128.09496,113.08406,114.04293,
         137.05891,87.03203,147.06841,113.08406,156.10111);

     expect_equal(fragmentIon(peptide.AA.weights)[[1]]$b, fragmentIon(peptide.AA)[[1]]$b, tolerance=1e-03)
     expect_equal(fragmentIon(peptide.AA.weights)[[1]]$y, fragmentIon(peptide.AA)[[1]]$y, tolerance=1e-03)
})

     
test_that("XGXFNAGVGK", {
     peptide <- "XGXFNAGVGK"
     fi <- fragmentIon(c("XGXFNAGVGK"))[[1]]
     pim <- parentIonMass(peptide)

     expect_equal(fi$b[2:8] + fi$y[8:2], rep(pim + 1.008, 7), tolerance=1e-03)
})