Faster quantify functions

[lgatto]

Quantification needs to be reimplemented at the C-level or using on disk access and using basic data types to make full use of the OnDiskMSnExp data structure.

Quantitation involves peak integration, which will be useful for MS1 and MS2 quantitation. The way this is done will depend if data is centroided (only really relevant for MS2 data) or profile mode. When in profile mode, the peak is a curve; in centroided mode, the peak is a sticky peak.

What follows is a crude description of the needs. I will refine later.

quantify

• To quantify a peak, first find it
• The peak is defined by on mz value and a tolerance, defining an mz
  range
• findPeak(mz, tolerance)

quantify(method = "max")

• default for centroided data, but also applicable to profile data
• return the max of the peak

quantify(method = "trapezoidation")

• calculate the area below the peak/curve
• here, we need to know where the curve starts and ends (mz range)
• here, we can be strict or not

findPeak(mz, tolerance)

• define the mz range
• To find the peak, look in the mz range and find the highest value. SeeMALDIquant:::.localMaxima, with appropriate halfWindowSize.
• If centroided, return the corresonding intensity and done.
• If profile, it's not a sticky peak, but a curve, and we still might
  want to to find the lower/left and upper/right ends of the curve to integrate.

Summary of quantify methods:

method	centroided	profile
trapezoidation	Not relevant, should use max	[1]
max	fastquant_max	[1]
sum		[1]
SI	SI	same
SIgi	SI	same
SIn	SI	same
SAF	SAF	same
NSAF	SAF	same
count	count_MSnSet	same
tic [2]	tic_MSnSet	same

Some functions are the same (after minor modifications) than for the MSnExp: count_MSnSet, tic_MSnSet, SI and SAF.

[1] this one could actually climb up outide of mz+/- wd to detect to maximum.
[2] actually not directly available as a method, used by SI, SIgi and SIn.

[lgatto]

For completeness, here's some testing/devel code I wrote that made it into MSnbase as the fastquant_max and quantify_OnDiskMSnExp_max functions (ad42601 and 55d3fac).

## quantifies peak pk in regions [pk - wd, pk + wd] at half window
## size hws in spectrum spi in file f using max of peak (irrespective
## if spectrum is centroided or profile mode)
fastquant_1 <- function(f, pk, spi, hws, wd = 1) {
    ramp <- new(mzR:::.__C__Rcpp_Ramp)
    ramp$open(f, declaredOnly = TRUE)
    if (!ramp$OK())
        stop("Unable to create valid cRamp object.")
    on.exit(ramp$close())
    pks <- ramp$getPeakList(spi)$peaks
    pks <- pks[pks[, 1] >= pk - wd & pks[, 1] <= pk + wd, ]
    mx <- MALDIquant:::.localMaxima(pks[, 2], hws)
    pks[mx, 2]
}


fastquant(x2[[372]], reporters = TMT6[1], method = "max")[[1]]

##        TMT6.126 TMT6.127 TMT6.128 TMT6.129 TMT6.130 TMT6.131
## X422.1 56807640 60283748 63901644 57897180 54275908 53960332

fastquant_1(f, 126, 422, 20)
fastquant_1(f, 127, 422, 20)
fastquant_1(f, 128, 422, 20)
fastquant_1(f, 129, 422, 20)
fastquant_1(f, 130, 422, 20)
fastquant_1(f, 131, 422, 20)


r1 <- quantify(x2[[372]], reporters = TMT6[1], method = "max")[[1]]
names(r1) <- NULL
r2 <- fastquant_1(f, 126, 422, 20)
identical(r1, r2)

microbenchmark(quantify(x2[[372]], reporters = TMT6, method = "max")[[1]],
               fastquant_1(f, 126, 422, 20),
               times = 10)

## quantifies peaks pk in regions [pks - wd, pks + wd] at half window
## size hws in spectrum spi in file f using max of peak (irrespective
## if spectrum is centroided or profile mode)
fastquant_n <- function(f, pk, spi, hws, wd = 1) {
    ramp <- new(mzR:::.__C__Rcpp_Ramp)
    ramp$open(f, declaredOnly = TRUE)
    if (!ramp$OK())
        stop("Unable to create valid cRamp object.")
    on.exit(ramp$close())
    pks <- ramp$getPeakList(spi)$peaks
    res <- rep(NA_real_, length(pk))
    for (ii in seq_along(pk)) {
        k <- pks[, 1] >= pk[ii] - wd & pks[, 1] <= pk[ii] + wd
        .pks <- pks[k, , drop = FALSE]
        mx <- MALDIquant:::.localMaxima(.pks[, 2], hws)
        res[ii] <- .pks[mx, 2]
    }
    res
}

quantify(x2[[372]], reporters = TMT6, method = "max")[[1]]
fastquant_n(f, pk = mz(TMT6), 422, 20)

r1 <- quantify(x2[[372]], reporters = TMT6, method = "max")[[1]]
names(r1) <- NULL
r2 <- fastquant_n(f, mz(TMT6), 422, 20, wd = 0.5)
identical(r1, r2)


microbenchmark(quantify(x2[[372]], reporters = TMT6, method = "max")[[1]],
               fastquant_n(f, mz(TMT6), 422, 20, wd = 0.5),
               times = 1)

## quantifies peaks pk in regions [pks - wd, pks + wd] at half window
## size hws in spectra spi in file f using max of peak (irrespective
## if spectrum is centroided or profile mode)
fastquant_nn <- function(f, pk, spi, hws, wd = 0.5) {
    ramp <- openMSfile(f)
    on.exit(close(ramp))
    pks <- peaks(ramp, spi)
    res <- matrix(NA_real_,
                  ncol = length(pk),
                  nrow = length(pks))
    for (i in seq_along(pks)) {
        for (ii in seq_along(pk)) {
            k <- pks[[i]][, 1] >= pk[ii] - wd & pks[[i]][, 1] <= pk[ii] + wd
            if (any(k)) {
                .pks <- pks[[i]][k, , drop = FALSE]
                mx <- MALDIquant:::.localMaxima(.pks[, 2], hws)
                res[i, ii] <- .pks[mx, 2]
            }
        }
    }
    res
}


library("MSnbase")
x2 <- readMSData2(f, msLevel = 2, centroided = TRUE)
ii <- fData(x2)$spIdx

library("microbenchmark")
microbenchmark(r1 <- quantify(x2, reporters = TMT6, verbose = FALSE,
                              method = "max", BPPARAM = SerialParam()),
               r2 <- fastquant_nn(f, pk = mz(TMT6), spi = ii, hws = 20L, wd = 0.05),
               times = 5)
## Unit: milliseconds
##        min         lq       mean     median         uq       max neval
## 18720.0183 18758.3670 22544.4527 19908.1385 27524.8491 27810.891     5
##   468.5377   471.3297   517.8705   472.1369   577.6511   599.697     5

##        min        lq       mean     median         uq        max neval
## 18695.8108 18908.834 19187.2583 18963.9148 19216.6528 20151.0787     5
##   468.3613   469.569   471.0501   471.4552   471.9763   473.8886     5

r1 <- exprs(r1)
attributes(r1) <- attributes(r1)[1]
identical(r1, r2)

## Code to inspect if not identical
sel <- !is.na(r1) & !is.na(r2)
r1[!sel] <- 0
r2[!sel] <- 0

table(r1 == r2)
kk <- arrayInd(which(!r1 == r2), dim(r1))
i <- sort(unique(kk[, 1]))
r1[i, ]
r2[i, ]
ssp <- lapply(spectra(x2[i]), as, "data.frame")
for (j in 1:length(ssp)) {
    x <- ssp[[j]]
    x <- x[x[, 1] > 120 & x[, 1] < 132, ]
    plot(x, type = "h", xlim = c(125, 132), ylim = c(0, max(x, 2)))
    grid()
    abline(v = mz(TMT6), col = "red", lty = "dotted")
    points(mz(TMT6), r1[i[j], ])
    points(mz(TMT6), r2[i[j], ], col = "red", pch = 3)
    tmp <- rbind(r1[i[j], ], r2[i[j], ])
    colnames(tmp) <- mz(TMT6)
    print(tmp)
    scan()
}

f2 <- "~/Data2/PXD000001-new-files/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML"
library("MSnbase")
x2 <- readMSData2(f, msLevel = 2, centroided = TRUE)
x <- readMSData(f, msLevel = 2, centroided = TRUE)

qe0 <- quantify(x, reporters = TMT6, verbose = FALSE, method = "max")
qe00 <- quantify(x2, reporters = TMT6, verbose = FALSE, method = "max")
all.equal(exprs(qe0), exprs(qe00), check.attributes = FALSE)

x2 <- readMSData2(f2, msLevel = 2, centroided = TRUE)
qe00 <- quantify(x2, reporters = TMT6, method = "max", BPPARAM = MulticoreParam(4L))
qe <- MSnbase:::fastquant_max(f2, pk = mz(TMT6), spi = fData(x2)$spIdx,
                              hws = 20L, wd = 0.05)

all.equal(qe, exprs(qe00), check.attributes = FALSE)

I will document these benchmarks in the benchmarking vignette (9902833).

[sgibb]

This is for TMT quantitation. So we are just interested in the highest peak in a reporter region (not in all local maxima). While MALDIquant:::.localMaxima is not needed here it could result in an error if the hws is too small. Minimal example that gives an error because of 2 local maxima:

## reporter mz
pk <- 10 
## stupid spectrum with two local maxima in a reporter region
pks <- list(cbind(mz=c(seq(9.2, 10.8, by=0.1)),
                  intensity=c(1:5, 4:1, 2:6, 5:3)))

## modified fastquant_max to work without a file
fastquant_max_org <- function(pks, pk, hws=20L, wd = 0.5) {
    res <- matrix(NA_real_,
                  ncol = length(pk),
                  nrow = length(pks))
    for (i in seq_along(pks)) {
        for (ii in seq_along(pk)) {
            k <- pks[[i]][, 1] >= pk[ii] - wd & pks[[i]][, 1] <= pk[ii] + wd
            if (any(k)) {
                .pks <- pks[[i]][k, , drop = FALSE]
                mx <- MALDIquant:::.localMaxima(.pks[, 2], hws)
                res[i, ii] <- .pks[mx, 2]
            }
        }
    }
    res
}
## small hws
fastquant_max_org(pks, pk, hws=2)
# Error in res[i, ii] <- .pks[mx, 2] :
#  number of items to replace is not a multiple of replacement length

I replaced MALDIquant:::.localMaxima with max (should be even faster) in c012ed9.

[lgatto]

Thanks @sgibb.

The function currently is used for iTRAQ/TMT quantitation indeed, but I would like it to be more general, or have one available for any peak (MS1 or MS2, centroided or profile). In your example, I would actually want the second max at M/Z 10.5 to be chosen. In that respect, the org function does have a bug, but I don't think using max would be the right change. Having said that, I think max is fine/better for the current limited use case (as we know the reporter mz values), and another function/iteration (for profile data) might revert to MALDIquant:::.localMaxima.