Reads a mgf file and generates an "MSnExp" object.
● Data Source:
BioConductor
● Keywords: file
● Alias: readMgfData
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This function can be used to create an "MSnSet" by reading and parsing an mzTab file. The metadata section is always used to populate the MSnSet's experimentData()@other$mzTab slot.
● Data Source:
BioConductor
● Keywords:
● Alias: readMzTabData
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This function can be used to create a "MSnSet" by reading and parsing an mzTab file. The metadata section is always used to populate the MSnSet's experimentData slot.
● Data Source:
BioConductor
● Keywords:
● Alias: readMzTabData_v0.9
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The method removes non-identifed features in MSnExp and MSnSet instances using relevant information from the feaureData slot of a user-provide filtering vector of logicals.
● Data Source:
BioConductor
● Keywords: methods
● Alias: removeNoId, removeNoId-methods
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This method sets low intensity peaks from individual spectra (Spectrum instances) or whole experiments (MSnExp instances) to 0. The intensity threshold is set with the t parameter. Default is the "min" character. The threshold is then set as the non-0 minimum intensity found in the spectrum. Any other numeric values is valid. All peaks with maximum intensity smaller or equal to t are set to 0.
● Data Source:
BioConductor
● Keywords: methods
● Alias: removePeaks-methods
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This methods sets all the reporter tag ion peaks from one MS2 spectrum or all the MS2 spectra of an experiment to 0. Reporter data is specified using an "ReporterIons" instance. The peaks are selected around the expected reporter ion m/z value +/- the reporter width. Optionally, the spectrum/spectra can be cleaned to remove successive 0 intensity data points (see the clean function for details).
● Data Source:
BioConductor
● Keywords: methods
● Alias: removeReporters, removeReporters-methods
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selectFeatureData
(Package: MSnbase) :
Select feature variables of interest
Select feature variables to be retained.
● Data Source:
BioConductor
● Keywords:
● Alias: selectFeatureData
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smooth-methods
(Package: MSnbase) :
Smooths 'MSnExp' or 'Spectrum' instances
This method smooths individual spectra (Spectrum instances) or whole experiments (MSnExp instances). Currently, the Savitzky-Golay-Smoothing (method = "SavitzkyGolay") and the Moving-Average-Smoothing (method = "MovingAverage") are available, as implemented in the MALDIquant::smoothIntensity function. Additional methods might be added at a later stage.
● Data Source:
BioConductor
● Keywords: methods
● Alias: smooth-methods
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trimMz-methods
(Package: MSnbase) :
Trims 'MSnExp' or 'Spectrum' instances
This method selects a range of MZ values in a single spectrum (Spectrum instances) or all the spectra of an experiment (MSnExp instances). The regions to trim are defined by the range of mzlim argument, such that MZ values < min(mzlim) and MZ values > max(mzlim) are trimmed away.
● Data Source:
BioConductor
● Keywords: methods
● Alias: trimMz-methods
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writeMgfData-methods
(Package: MSnbase) :
Write an experiment or spectrum to an mgf file
Methods writeMgfData write individual "Spectrum" instances of whole "MSnExp" experiments to a file in Mascot Generic Format (mgf) (see http://www.matrixscience.com/help/data_file_help.html for more details). Function readMgfData read spectra from and mgf file and creates an "MSnExp" object.
● Data Source:
BioConductor
● Keywords: file, methods
● Alias: writeMgfData, writeMgfData,MSnExp-method, writeMgfData,Spectrum-method, writeMgfData-methods
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