getMS2Mat: Extract a scan x mass matrix from xcmsRaw object(s).

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

Description

For the defined scans, this function identifies consensus masses based on a minimal signal intensity cut-off. Then a data.frame is returned with EICs in columns for each identified mass.

Usage

getMS2Mat(xraw, region = NULL, precursors = NULL, rtrange = NULL, collisionEnergy = NULL, ppm = 30, minSignal = 100)

Arguments

xraw	xcmsRaw object or list of xcmsRaw objects
region	rows from a peak table where the feature of interest was detected (optional)
precursors	the precursors that the mass spec targeted
rtrange	range of scans to use
collisionEnergy	the collision energy of the scans to use
ppm	ppm error mass variability between scans
minSignal	smallest intensity that could initiate a mass to include as column

Details

if precursors, rtrange, or collsionEnergy are left out or NULL, all values present in xraw are used

Value

ms2_mat

a data.frame containing a row for each scan, with: xcmsRaw: index of xcmsRaw file scan: scan number rt: retention time of scan ce: collision energy of scan prec: precursor that was targeted and a column for every mass.

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, region = NULL, precursors = NULL, rtrange = NULL,
    collisionEnergy = NULL, ppm = 30, minSignal = 100)
{
    if (!is.null(region)) {
        rtrange = c(min(region$rtmin) - 5, max(region$rtmax) +
            5)
    }
    if (class(xraw) == "xcmsRaw") {
        xraw = c(xraw)
    }
    scans = lapply(xraw, selectScans, precursors = precursors,
        rtrange = rtrange, collisionEnergy = collisionEnergy)
    combinedScans = combineScans(xraw, scans, minSignal)
    if (nrow(combinedScans) > 2) {
        cons_masses = getConsensusMasses(combinedScans, ppm = ppm)
        ms2_mat = createMatrix(xraw, scans, cons_masses, ppm = ppm)
        return(ms2_mat)
    }
    else {
        cat("ms2 has no masses with intensity above: ", minSignal,
            "\n")
    }
  }

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