getMS1Mat: Extract dected masses from a subset of MS1 scans in xcmsRaw...

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

Description

Identify masses using kernel density of centroided data.

Usage

getMS1Mat(xraw, rtrange = NULL, ppm = 25, minSignal = 400)

Arguments

xraw	an xcms raw object
rtrange	range of retention times of scans
ppm	mass deviation between scans for obtaining EIC for each mass
minSignal	lowest signal intensity that could be considered a mass

Value

ms1_mat

matrix where the rows are scans (ordered by retention time) and columns are masses

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 (xraw, rtrange = NULL, ppm = 25, minSignal = 400)
{
    if (is.null(rtrange)) {
        scans = 1:length(xraw@scantime)
    }
    else {
        scans = which(xraw@scantime >= rtrange[1] & xraw@scantime <=
            rtrange[2])
    }
    combinedScans = do.call(rbind, sapply(scans, getScan, object = xraw))
    cons_masses = getConsensusMasses(combinedScans, ppm = ppm)
    ms1_mat = c()
    for (s in scans) {
        scan = getScan(xraw, s)
        intensities = sapply(cons_masses, function(m) {
            matches = ppm_diff(m, scan[, "mz"]) < ppm
            if (any(matches))
                return(max(scan[matches, "intensity"]))
            else return(0)
        })
        ms1_mat = rbind(ms1_mat, intensities)
    }
    colnames(ms1_mat) = cons_masses
    rownames(ms1_mat) = round(xraw@scantime[scans], 2)
    ms1_mat
  }

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