Description Usage Arguments Details Value Author(s) See Also
View source: R/do_findChromPeaks-functions.R
The do_findChromPeaks_centWaveWithPredIsoROIs
performs a
two-step centWave based peak detection: chromatographic peaks are
identified using centWave followed by a prediction of the location of
the identified peaks' isotopes in the mz-retention time space. These
locations are fed as regions of interest (ROIs) to a subsequent
centWave run. All non overlapping peaks from these two peak detection
runs are reported as the final list of identified peaks.
The do_findChromPeaks_centWaveAddPredIsoROIs
performs
centWave based peak detection based in regions of interest (ROIs)
representing predicted isotopes for the peaks submitted with argument
peaks.
. The function returns a matrix with the identified peaks
consisting of all input peaks and peaks representing predicted isotopes
of these (if found by the centWave algorithm).
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 | do_findChromPeaks_centWaveWithPredIsoROIs(
mz,
int,
scantime,
valsPerSpect,
ppm = 25,
peakwidth = c(20, 50),
snthresh = 10,
prefilter = c(3, 100),
mzCenterFun = "wMean",
integrate = 1,
mzdiff = -0.001,
fitgauss = FALSE,
noise = 0,
verboseColumns = FALSE,
roiList = list(),
firstBaselineCheck = TRUE,
roiScales = NULL,
snthreshIsoROIs = 6.25,
maxCharge = 3,
maxIso = 5,
mzIntervalExtension = TRUE,
polarity = "unknown",
extendLengthMSW = FALSE
)
do_findChromPeaks_addPredIsoROIs(
mz,
int,
scantime,
valsPerSpect,
ppm = 25,
peakwidth = c(20, 50),
snthresh = 6.25,
prefilter = c(3, 100),
mzCenterFun = "wMean",
integrate = 1,
mzdiff = -0.001,
fitgauss = FALSE,
noise = 0,
verboseColumns = FALSE,
peaks. = NULL,
maxCharge = 3,
maxIso = 5,
mzIntervalExtension = TRUE,
polarity = "unknown"
)
|
mz |
Numeric vector with the individual m/z values from all scans/ spectra of one file/sample. |
int |
Numeric vector with the individual intensity values from all scans/spectra of one file/sample. |
scantime |
Numeric vector of length equal to the number of spectra/scans of the data representing the retention time of each scan. |
valsPerSpect |
Numeric vector with the number of values for each spectrum. |
ppm |
|
peakwidth |
|
snthresh |
For |
prefilter |
|
mzCenterFun |
Name of the function to calculate the m/z center of the
chromatographic peak. Allowed are: |
integrate |
Integration method. For |
mzdiff |
|
fitgauss |
|
noise |
|
verboseColumns |
|
roiList |
An optional list of regions-of-interest (ROI) representing
detected mass traces. If ROIs are submitted the first analysis step is
omitted and chromatographic peak detection is performed on the submitted
ROIs. Each ROI is expected to have the following elements specified:
|
firstBaselineCheck |
|
roiScales |
Optional numeric vector with length equal to |
snthreshIsoROIs |
|
maxCharge |
|
maxIso |
|
mzIntervalExtension |
|
polarity |
|
extendLengthMSW |
Option to force centWave to use all scales when
running centWave rather than truncating with the EIC length. Uses the "open"
method to extend the EIC to a integer base-2 length prior to being passed to
|
peaks. |
A matrix or |
For more details on the centWave algorithm see
centWave
.
A matrix, each row representing an identified chromatographic peak. All non-overlapping peaks identified in both centWave runs are reported. The matrix columns are:
Intensity weighted mean of m/z values of the peaks across scans.
Minimum m/z of the peaks.
Maximum m/z of the peaks.
Retention time of the peak's midpoint.
Minimum retention time of the peak.
Maximum retention time of the peak.
Integrated (original) intensity of the peak.
Per-peak baseline corrected integrated peak intensity.
Maximum intensity of the peak.
Signal to noise ratio, defined as (maxo - baseline)/sd
,
sd
being the standard deviation of local chromatographic noise.
RMSE of Gaussian fit.
Additional columns for verboseColumns = TRUE
:
Gaussian parameter mu.
Gaussian parameter sigma.
Gaussian parameter h.
Region number of the m/z ROI where the peak was localized.
m/z deviation of mass trace across scans in ppm.
Scale on which the peak was localized.
Peak position found by wavelet analysis (scan number).
Left peak limit found by wavelet analysis (scan number).
Right peak limit found by wavelet analysis (scan numer).
Hendrik Treutler, Johannes Rainer
Other core peak detection functions:
do_findChromPeaks_centWave()
,
do_findChromPeaks_massifquant()
,
do_findChromPeaks_matchedFilter()
,
do_findPeaks_MSW()
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