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 = c(85, 500), Window = 5, IntThreshold = 10, pp.method = "smoothing")
cdfFile |
A character string naming a netcdf file. |
massRange |
A two component numeric vector with the scan mass range to extract. |
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" and "ppc" . |
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.
The massRange
parameter is a numeric vector with two components: lower
and higher masses. All masses in that range will be extracted. Note that it is
not possible to extract a discontinuous mass range.
There are two peak picking algorithms that can be used. The "smoothing"
method
smooths the m/z curves and then looks for a change of sign of the intensity difference
between two consecutive points. The "ppc"
uses a sliding window and looks
for the local maxima. This method is based on R-package ppc
.
A two 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. |
Alvaro Cuadros-Inostroza, Matthew Hannah, Henning Redestig
require(TargetSearchData) data(TargetSearchData) CDFpath <- file.path(.find.package("TargetSearchData"), "gc-ms-data") CDFfiles <- dir(CDFpath, pattern = "\.cdf$", full.names = TRUE) CDFfiles # extrac peaks of first chromatogram peaks.1 <- NetCDFPeakFinding(CDFfiles[1], massRange = c(85, 320), Window = 15, IntThreshold = 10, pp.method = "smoothing") # scan acquisition times head(peaks.1$Time) # peaks in matrix form. first column is mass 85, last one is mass 320. head(peaks.1$Peaks)