deconvolveSources: Deconvolves the mixed scans in ms2_mat returned by getMS2Mat

In yufree/decoMS2: Deconvolution of heterogeneous MS2 spectra collected for metabolite identification in untargeted metabolomics experiments.

Description

Uses non-negative least squares to find the most likely portion of each observed mass that was contributed by each precursor in each scan

Usage

deconvolveSources(ms2_mat, precursors, windowOffSet = c(-1, 9), deisotope = T, intensityFilter = 0.05, cole = 20)

Arguments

ms2_mat	data.frame returned by getMS2Mat
precursors	the precursors that were targeted
windowOffSet	window offset for the instrument that gives the bounds of the isolation window. Used to define which columns could potentially be precursors.
deisotope	remove potential isotope precursors
intensityFilter	minimal relative intensity for a precursor
cole	collsiion energy that contains non0V scans

Details

Most useful parameter to tinker with is the intensityFilter

Value

sources

a matrix with a row for each source and column for each mass. Plot each row with plot_source.

Author(s)

Igor Nikolskiy

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (ms2_mat, precursors, windowOffSet = c(-1, 9), deisotope = T,
    intensityFilter = 0.05, cole = 20)
{
    precMat = subset_ms2_mat(ms2_mat, prec = precursors, cole = 0)
    cols = grep("[0-9]+.[0-9]+", colnames(precMat))
    masses = as.numeric(colnames(precMat)[cols])
    possiblePrecs = min(precursors) + windowOffSet[1] < masses &
        max(precursors) + windowOffSet[2] > masses
    cols = cols[possiblePrecs]
    masses = as.numeric(colnames(precMat)[cols])
    if (deisotope) {
        isos = findIsotopeMasses(masses)
        if (any(isos))
            cols = cols[-isos]
    }
    interpolated = c()
    observations = c()
    for (xr in unique(ms2_mat$xcmsRaw)) {
        for (p in unique(ms2_mat$prec)) {
            om = subset_ms2_mat(ms2_mat, prec = p, cole = cole,
                xr = xr)
            pm = subset_ms2_mat(ms2_mat, prec = p, cole = 0,
                xr = xr)
            loc = apply(pm[, cols, drop = F], 2, function(x) {
                interpolatePrecursor(x, rownames(pm), rownames(om))
            })
            interpolated = rbind(interpolated, loc)
            observations = rbind(observations, om)
        }
    }
    cols = max(interpolated) * intensityFilter < apply(interpolated,
        2, max)
    interpolated = interpolated[, cols, drop = F]
    sources = sapply(apply(observations, 2, nnls, A = interpolated),
        function(x) x$x)
    if (!is.null(dim(sources))) {
        rownames(sources) = colnames(interpolated)
    }
    sources
  }

yufree/decoMS2 documentation built on May 27, 2019, 9:56 a.m.