NetCDFPeakFinding: Peak picking algorithm from CDF files

In acinostroza/TargetSearch: A package for the analysis of GC-MS metabolite profiling data

Peak picking algorithm from CDF files

Description

This function reads a netcdf chromatogram file, finds the apex intensities and returns a list containing the retention time and the intensity matrices.

Usage

NetCDFPeakFinding(ncdf, massRange = NULL, Window = 15, IntThreshold = 10,
                  pp.method = "ppc", baseline = FALSE, ...)

Arguments

ncdf	A character string naming a netcdf file or a list generated by the function peakCDFextraction.
massRange	Deprecated. It is completely ignored but it is kept for compatibility with old scripts.
Window	The window used by peak picking method. The number of points actually used is 2*Window + 1.
IntThreshold	Apex intensities lower than this value will be removed from the RI files.
pp.method	The pick picking method to be used. Options are "smoothing", "gaussian" and "ppc".
baseline	Logical. Should baseline correction be performed?
...	Extra options passed to baseline.

Details

The parameter ncdf should be either a path to a NetCDF file or a list generated by the function peakCDFextraction. This list contains elements named "Time", "Peaks", "massRange", "Index", and "baselineCorrected". Refer to the function's man page for details.

Formerly, the massRange parameter was a numeric vector with two components: lower and higher masses. Now, the mass range is detected automatically and it has no effect if it is set. It is kept only for compatibility reasons.

There are three peak picking algorithms that can be used. The "smoothing" method smooths the m/z curves by a moving average and then looks for a change of sign of the intensity difference between two consecutive points. The "gaussian" is exactly the same, but it uses a gaussian smoother instead of a moving average.

The "ppc" uses a sliding window and looks for the local maxima. This method is based on the R-package ppc (now unavailable).

Value

A three component list.

Time	The retention time vector.
Peaks	The intensity matrix. Rows are the retention times and columns are masses. The first column is the lower mass value and the last one is the higher mass.
massRange	The mass range.

Author(s)

Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig

See Also

peakCDFextraction

Examples

require(TargetSearchData)
# pick first CDF file
CDFfile <- tsd_cdffiles()[1]

# extract peaks of first chromatogram
peaks.1 <- NetCDFPeakFinding(CDFfile, Window = 15, IntThreshold = 10, pp.method = "ppc")
# scan acquisition times
head(peaks.1$Time)
# peaks in matrix form. first column is mass 85, last one is mass 320.
head(peaks.1$Peaks)

acinostroza/TargetSearch documentation built on Nov. 22, 2024, 3:31 p.m.