SCPeakRegions: Holds all the peak region data
In MoseleyBioinformaticsLab/ScanCentricPeakCharacterization: Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner
SCPeakRegions R Documentation
Holds all the peak region data
Description
Holds all the peak region data
Holds all the peak region data
Details
This reference class represents the peak region data.
Public fields
frequency_point_regionsthe frequency data
frequency_fit_descriptionthe model of frequency ~ m/z
mz_fit_descriptionthe model of m/z ~ frequency
peak_regionsthe peak regions
sliding_regionsthe sliding regions used for density calculations
tiled_regionsthe tiled regions used for grouping and splitting peak regions
peak_region_listlist of regions
frequency_multiplierhow much to multiplier frequency by to make interval points
scan_peaksthe peaks by scans
peak_datathe data.frame of final peak data
scan_level_arraysscan level peak data as matrices
is_normalizedare the peak intensities normalized
normalization_factorsthe normalization factors calculated
n_scanhow many scans are we working with
scans_per_peak??
scan_percwhat percentage of scans is a minimum
min_scanbased on scan_perc, how many scans minimum does a peak
need to be in
max_subsets??
scan_subsets??
frequency_rangewhat is the range in frequency space
scan_correlation??
keep_peakswhich peaks are we keeping out of all the peaks we had
peak_indexthe indices for the peaks
scan_indicesthe names of the scans
instrumentthe instrument serial number if available
Methods
Public methods
Method set_min_scan()
sets the minimum number of scans to use
Usage
SCPeakRegions$set_min_scan()
Method add_data()
Adds the data from an SCMzml object to the SCPeakRegion.
Usage
SCPeakRegions$add_data(sc_mzml)
Arguments
sc_mzmlthe SCMzml object being passed in
Method new()
Creates a new SCPeakRegions object
Usage
SCPeakRegions$new(
sc_mzml = NULL,
frequency_multiplier = 400,
scan_perc = 0.1,
max_subsets = 100
)
Arguments
sc_mzmlthe SCMzml object to get data from
frequency_multiplierhow much to multiply frequency by
scan_perchow many scans are required to be in to be a "peak"
max_subsets??
Method clone()
The objects of this class are cloneable with this method.
Usage
SCPeakRegions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
MoseleyBioinformaticsLab/ScanCentricPeakCharacterization documentation built on March 29, 2024, 11:32 p.m.
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| SCPeakRegions | R Documentation |
Holds all the peak region data
Description
Holds all the peak region data
Holds all the peak region data
Details
This reference class represents the peak region data.
Public fields
frequency_point_regionsthe frequency data
frequency_fit_descriptionthe model of frequency ~ m/z
mz_fit_descriptionthe model of m/z ~ frequency
peak_regionsthe peak regions
sliding_regionsthe sliding regions used for density calculations
tiled_regionsthe tiled regions used for grouping and splitting peak regions
peak_region_listlist of regions
frequency_multiplierhow much to multiplier frequency by to make interval points
scan_peaksthe peaks by scans
peak_datathe data.frame of final peak data
scan_level_arraysscan level peak data as matrices
is_normalizedare the peak intensities normalized
normalization_factorsthe normalization factors calculated
n_scanhow many scans are we working with
scans_per_peak??
scan_percwhat percentage of scans is a minimum
min_scanbased on
scan_perc, how many scans minimum does a peak need to be inmax_subsets??
scan_subsets??
frequency_rangewhat is the range in frequency space
scan_correlation??
keep_peakswhich peaks are we keeping out of all the peaks we had
peak_indexthe indices for the peaks
scan_indicesthe names of the scans
instrumentthe instrument serial number if available
Methods
Public methods
Method set_min_scan()
sets the minimum number of scans to use
Usage
SCPeakRegions$set_min_scan()
Method add_data()
Adds the data from an SCMzml object to the SCPeakRegion.
Usage
SCPeakRegions$add_data(sc_mzml)
Arguments
sc_mzmlthe SCMzml object being passed in
Method new()
Creates a new SCPeakRegions object
Usage
SCPeakRegions$new( sc_mzml = NULL, frequency_multiplier = 400, scan_perc = 0.1, max_subsets = 100 )
Arguments
sc_mzmlthe SCMzml object to get data from
frequency_multiplierhow much to multiply frequency by
scan_perchow many scans are required to be in to be a "peak"
max_subsets??
Method clone()
The objects of this class are cloneable with this method.
Usage
SCPeakRegions$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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