NetCDFPeakFinding {TargetSearch}R Documentation

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

Arguments

cdfFile

A character string naming a netcdf file.

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?

baseline.opts

A list of options passed to baselineCorrection

.

Details

The function expects the following NetCDF variables: intensity_values, mass_values, scan_index, point_count and scan_acquisition_time. Otherwise, an error will be displayed.

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 R-package ppc.

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)
CDFpath <- file.path(find.package("TargetSearchData"), "gc-ms-data")
CDFfiles <- dir(CDFpath, pattern = ".cdf$", full.names = TRUE)
CDFfiles

# extrac peaks of first chromatogram
peaks.1 <- NetCDFPeakFinding(CDFfiles[1], Window = 15, IntThreshold = 10, pp.method = "smoothing")
# 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)


[Package TargetSearch version 1.40.3 Index]