inst/unitTests/test_genSwathIonLib.R

In specL: specL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics

#R
# $HeadURL$
# $Id$
# $Date$

test_genSwathIonLib <-
function(){
# TEST 1
    r.genSwathIonLib.top5 <- genSwathIonLib(peptideStd,
        peptideStd.redundant, topN=5, 
        fragmentIonRange=c(2,100),
        fragmentIonMzRange=c(200,2000),
        fragmentIonFUN=function (b, y) {
            return( cbind(y1_=y) )
        }
    )
    
    checkEqualsNumeric(r.genSwathIonLib.top5@ionlibrary[[40]]@q3, 
        c(800.4497, 604.3285,1016.5222, 503.2805, 929.4925),
        tolerance = 0.001)

    checkEqualsNumeric(r.genSwathIonLib.top5@rt.input[1:5], 
        c(16.83185, 13.13262, 18.54058, 18.36923, 15.30478), 
        tolerance = 0.001)
    
    checkEqualsNumeric(r.genSwathIonLib.top5@rt.normalized[1:5], 
        c(95.97314, 52.60417, 116.00582, 113.99703,  78.07007), 
        tolerance = 0.001)

    checkEqualsNumeric(length(r.genSwathIonLib.top5@rt.normalized), 
        length(r.genSwathIonLib.top5@rt.normalized), 
        tolerance = 0.001)
}

test_genSwathIonLib_noiRT_peptides <-
function(){
    # case 1: useless peptides

    #reverse n iRT peptides
    n <- 7
    peptide <- unlist(lapply(as.character(iRTpeptides$peptide[1:n]),
                             function(x){paste(rev(strsplit(x,"")[[1]]), collapse='')})) 
    
    rt <- seq(-24.9200, 122.2462, length=length(peptide))
    myiRTpeptides<-cbind(peptide=peptide, rt=rt)

    peptideStd.ionLib <- genSwathIonLib(data=peptideStd, 
                                        data.fit=peptideStd.redundant, 
                                        iRT=myiRTpeptides)

    # add cmp for idx should be always 137
    # 
    res <- lapply (1:length(peptideStd), 
        function(idx){ 
            checkEqualsNumeric(ionlibrary(peptideStd.ionLib)[[idx]]@irt, 
                peptideStd[[idx]]$rt, 
                tolerance=0.05)
            }
            )
}

test_genSwathIonLib_swath_windows  <-
function(){
    myFragmentIon <- function (b, y) {
        Hydrogen <- 1.007825
        Oxygen <- 15.994915
        Nitrogen <- 14.003074
        b1_ <- (b )
        y1_ <- (y ) 
        b2_ <- (b + Hydrogen) / 2
        y2_ <- (y + Hydrogen) / 2 
        b3_ <- (b + 2 * Hydrogen) / 3
        y3_ <- (y + 2 * Hydrogen) / 3
        return( cbind(b1_, y1_, b2_, y2_, b3_, y3_) )
                                                                                            }
       idx <- 135

    il.default <- genSwathIonLib(data=peptideStd[idx],
        data.fit=peptideStd.redundant,
        fragmentIonRange=c(5,10),
        topN=5,
        fragmentIonFUN=myFragmentIon)

    il.swath_windows <- genSwathIonLib(data = peptideStd[idx],
        data.fit = peptideStd.redundant,
        fragmentIonRange = c(5, 10),
        topN = 5,
        breaks = seq(400, 2000, by=25),
        fragmentIonFUN=myFragmentIon)

    breaks <- seq(400, 2000, by = 25)
    
    # use case 1 using the breaks option
    x <- ionlibrary(il.swath_windows)[[1]]
    
    q1_idx <- lower_bound_(x@q1, breaks)
    q3_idx <- lower_bound_(x@q3, breaks)
    
    checkTrue(q1_idx == 32)
    
    checkTrue(q1_idx %in% q3_idx == FALSE)
    
    lapply(x@frg_type == c('y', 'y', 'y', 'y', 'b'), function(x){checkTrue(x)} )

    lapply(x@frg_nr == c(12, 15, 10, 14, 4), function(x){checkTrue(x)} )

    lapply(round(x@relativeFragmentIntensity) == c(100, 60, 56, 40, 23), function(x){checkTrue(x)} )

    # use case 2 
    x <- ionlibrary(il.default)[[1]]
    
    # compute collision ions, should be id 32
    q1_idx <- lower_bound_(x@q1, breaks)
    q3_idx <- lower_bound_(x@q3, breaks)

    checkTrue(q1_idx == 32)
    lapply (q3_idx == c(35, 50, 29, 32, 46), function(x){checkTrue(x)} )
}

test_genSwathIonLib()
test_genSwathIonLib_noiRT_peptides()
test_genSwathIonLib_swath_windows()

# TODO(cp):
# check lower boundary of transitions
# genSwathIonLib(peptideStd, peptideStd.redundant, topN=15, fragmentIonRange=c(12, 20))
# nur alle peptide die mind. 12 assigneed fragment ions max 15