NetCDFPeakFinding {TargetSearch} | R Documentation |
This function reads a netcdf chromatogram file, finds the apex intensities and returns a list containing the retention time and the intensity matrices.
NetCDFPeakFinding(cdfFile, massRange = NULL, Window = 15, IntThreshold = 10, pp.method = "ppc", baseline = FALSE, baseline.opts = NULL)
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 |
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 |
baseline |
Logical. Should baseline correction be performed? |
baseline.opts |
A list of options passed to |
.
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
.
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. |
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
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)