SCMzml: R6 Class For mzML Data
In MoseleyBioinformaticsLab/ScanCentricPeakCharacterization: Functionality for Characterizing Peaks in Mass Spectrometry in a Scan-Centric Manner
SCMzml R Documentation
R6 Class For mzML Data
Description
mzML mass spectrometry data container with some useful methods.
Details
Provides our own container for mzML data, and does conversion to frequency,
filtering scans, choosing a single frequency regression model, and
generating the frequency data for use in the peak characterization.
Public fields
mzml_filethe mzml file location
mzml_metadatametadata from an external json file
mzml_datathe actual mzml data from MSnbase
mzml_df_dataa list of data.frames of the data
scan_rangethe range of scans to be used
rtime_rangethe range of retention times to keep
mz_rangethe mz range to use
scan_infodata.frame of scan information
remove_zeroshould zero intensity data points be removed?
frequency_fit_descriptionthe model for m/z -> frequency
mz_fit_descriptionthe model for going from frequency -> m/z
frequency_coefficientsthe coefficients for the frequency model
mz_coefficientsthe coefficients for the m/z model
ms_levelwhich MS level will we be using from the mzml file?
memory_modehow will the mzml data be worked with to start, inMemory or onDisk?
difference_rangehow wide to consider adjacent frequency points as good
choose_frequency_model_functionwhere the added model selection function will live
filter_scan_functionwhere the added filter scan function will live.
choose_single_frequency_modelfunction to choose a single frequency model
Methods
Public methods
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Method import_mzml()
import the mzml file defined
Usage
SCMzml$import_mzml(
mzml_file = self$mzml_file,
ms_level = self$ms_level,
memory_mode = self$memory_mode
)
Arguments
mzml_filewhat file are we reading in?
ms_levelwhich ms level to import (default is 1)
memory_modeuse inMemory or onDisk mode
Method extract_mzml_data()
get the mzml data into data.frame form so we can use it
Usage
SCMzml$extract_mzml_data(remove_zero = self$remove_zero)
Arguments
remove_zerowhether to remove zero intensity points or not
Method predict_frequency()
predict frequency and generate some summary information.
This does regression of frequency ~ m/z for each scan separately.
Usage
SCMzml$predict_frequency(
frequency_fit_description = self$frequency_fit_description,
mz_fit_description = self$mz_fit_description
)
Arguments
frequency_fit_descriptionthe regression model definition
mz_fit_descriptionthe regression model definition
Method convert_to_frequency()
actually do the conversion of m/z to frequency
Usage
SCMzml$convert_to_frequency()
Method choose_frequency_model()
choose a frequency model using the previously added function
Usage
SCMzml$choose_frequency_model()
Method generate_choose_frequency_model_function()
generate a frequency model choosing function and attach it
Usage
SCMzml$generate_choose_frequency_model_function(f_function = NULL)
Arguments
f_functionthe function you want to pass in
Details
Creates a new function that access the scan_info slot of an SCMzml object
after conversion to frequency space, and chooses a single model based on the information
there.
Method filter_scans()
filter the scans using the previously added function
Usage
SCMzml$filter_scans()
Method generate_filter_scan_function()
generate a filter function and attach it
Usage
SCMzml$generate_filter_scan_function(
rtime = NA,
y.freq = NA,
f_function = NULL
)
Arguments
rtimeretention time limits of scans to keep (NA)
y.freqy-frequency coefficient limits of scans to keep (NA)
f_functiona full function to set as the filtering function
Details
Creates a new function that accesses the scan_info slot of
an SCMzml object, filters the scans by their retention-time and
y-frequency coefficients, tests for outliers in the y-frequency
coefficients, and denotes which scans will be kept for further
processing.
NA means no filtering will be done, one-sided limits, eg. (NA, 10) or (10, NA)
implies to filter <= or >=, respectively.
Method check_frequency_model()
check how well a given frequency model works for this data
Usage
SCMzml$check_frequency_model(scan = NULL, as_list = FALSE)
Arguments
scanwhich scan to show predictions for
as_listwhether plots should be returned as a single plot or a list of plots
Method get_instrument()
get instrument data from associated mzml file metadata
Usage
SCMzml$get_instrument()
Method get_frequency_data()
get the frequency data to go into the next steps of analysis.
Usage
SCMzml$get_frequency_data()
Method new()
Usage
SCMzml$new(
mzml_file,
frequency_fit_description = c(a.freq = 0, x.freq = -1, y.freq = -1/2, z.freq = -1/3),
mz_fit_description = c(a.mz = 0, x.mz = -1, y.mz = -2, z.mz = -3),
metadata_file = NULL,
scan_range = NULL,
rtime_range = NULL,
mz_range = NULL,
remove_zero = FALSE,
ms_level = 1,
memory_mode = "inMemory"
)
Arguments
mzml_filethe file to load and use
frequency_fit_descriptiona description of the regression model for frequency ~ m/z
mz_fit_descriptiona description of the regression model for m/z ~ frequency
metadata_filea metadata file generated by ...
scan_rangewhich scans can be used for analysis
rtime_rangethe retention time to use for scans
mz_rangewhat m/z range to use
remove_zeroshould zero intensity data be removed?
ms_levelwhat MS level should be extracted (default is 1)
memory_modewhat memory mode should MSnbase be using (inMemory or onDisk)
Method clone()
The objects of this class are cloneable with this method.
Usage
SCMzml$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
choose_single_frequency_model_default()
Examples
## Not run:
lipid_sample = system.file("extdata", "lipid_example.mzML",
package = "ScanCentricPeakCharacterization")
## End(Not run)
MoseleyBioinformaticsLab/ScanCentricPeakCharacterization documentation built on March 29, 2024, 11:32 p.m.
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| SCMzml | R Documentation |
R6 Class For mzML Data
Description
mzML mass spectrometry data container with some useful methods.
Details
Provides our own container for mzML data, and does conversion to frequency, filtering scans, choosing a single frequency regression model, and generating the frequency data for use in the peak characterization.
Public fields
mzml_filethe mzml file location
mzml_metadatametadata from an external json file
mzml_datathe actual mzml data from MSnbase
mzml_df_dataa list of data.frames of the data
scan_rangethe range of scans to be used
rtime_rangethe range of retention times to keep
mz_rangethe mz range to use
scan_infodata.frame of scan information
remove_zeroshould zero intensity data points be removed?
frequency_fit_descriptionthe model for m/z -> frequency
mz_fit_descriptionthe model for going from frequency -> m/z
frequency_coefficientsthe coefficients for the frequency model
mz_coefficientsthe coefficients for the m/z model
ms_levelwhich MS level will we be using from the mzml file?
memory_modehow will the mzml data be worked with to start, inMemory or onDisk?
difference_rangehow wide to consider adjacent frequency points as good
choose_frequency_model_functionwhere the added model selection function will live
filter_scan_functionwhere the added filter scan function will live.
choose_single_frequency_modelfunction to choose a single frequency model
Methods
Public methods
Method import_mzml()
import the mzml file defined
Usage
SCMzml$import_mzml( mzml_file = self$mzml_file, ms_level = self$ms_level, memory_mode = self$memory_mode )
Arguments
mzml_filewhat file are we reading in?
ms_levelwhich ms level to import (default is 1)
memory_modeuse inMemory or onDisk mode
Method extract_mzml_data()
get the mzml data into data.frame form so we can use it
Usage
SCMzml$extract_mzml_data(remove_zero = self$remove_zero)
Arguments
remove_zerowhether to remove zero intensity points or not
Method predict_frequency()
predict frequency and generate some summary information. This does regression of frequency ~ m/z for each scan separately.
Usage
SCMzml$predict_frequency( frequency_fit_description = self$frequency_fit_description, mz_fit_description = self$mz_fit_description )
Arguments
frequency_fit_descriptionthe regression model definition
mz_fit_descriptionthe regression model definition
Method convert_to_frequency()
actually do the conversion of m/z to frequency
Usage
SCMzml$convert_to_frequency()
Method choose_frequency_model()
choose a frequency model using the previously added function
Usage
SCMzml$choose_frequency_model()
Method generate_choose_frequency_model_function()
generate a frequency model choosing function and attach it
Usage
SCMzml$generate_choose_frequency_model_function(f_function = NULL)
Arguments
f_functionthe function you want to pass in
Details
Creates a new function that access the scan_info slot of an SCMzml object
after conversion to frequency space, and chooses a single model based on the information
there.
Method filter_scans()
filter the scans using the previously added function
Usage
SCMzml$filter_scans()
Method generate_filter_scan_function()
generate a filter function and attach it
Usage
SCMzml$generate_filter_scan_function( rtime = NA, y.freq = NA, f_function = NULL )
Arguments
rtimeretention time limits of scans to keep (NA)
y.freqy-frequency coefficient limits of scans to keep (NA)
f_functiona full function to set as the filtering function
Details
Creates a new function that accesses the scan_info slot of
an SCMzml object, filters the scans by their retention-time and
y-frequency coefficients, tests for outliers in the y-frequency
coefficients, and denotes which scans will be kept for further
processing.
NA means no filtering will be done, one-sided limits, eg. (NA, 10) or (10, NA)
implies to filter <= or >=, respectively.
Method check_frequency_model()
check how well a given frequency model works for this data
Usage
SCMzml$check_frequency_model(scan = NULL, as_list = FALSE)
Arguments
scanwhich scan to show predictions for
as_listwhether plots should be returned as a single plot or a list of plots
Method get_instrument()
get instrument data from associated mzml file metadata
Usage
SCMzml$get_instrument()
Method get_frequency_data()
get the frequency data to go into the next steps of analysis.
Usage
SCMzml$get_frequency_data()
Method new()
Usage
SCMzml$new( mzml_file, frequency_fit_description = c(a.freq = 0, x.freq = -1, y.freq = -1/2, z.freq = -1/3), mz_fit_description = c(a.mz = 0, x.mz = -1, y.mz = -2, z.mz = -3), metadata_file = NULL, scan_range = NULL, rtime_range = NULL, mz_range = NULL, remove_zero = FALSE, ms_level = 1, memory_mode = "inMemory" )
Arguments
mzml_filethe file to load and use
frequency_fit_descriptiona description of the regression model for frequency ~ m/z
mz_fit_descriptiona description of the regression model for m/z ~ frequency
metadata_filea metadata file generated by ...
scan_rangewhich scans can be used for analysis
rtime_rangethe retention time to use for scans
mz_rangewhat m/z range to use
remove_zeroshould zero intensity data be removed?
ms_levelwhat MS level should be extracted (default is 1)
memory_modewhat memory mode should MSnbase be using (inMemory or onDisk)
Method clone()
The objects of this class are cloneable with this method.
Usage
SCMzml$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
choose_single_frequency_model_default()
Examples
## Not run:
lipid_sample = system.file("extdata", "lipid_example.mzML",
package = "ScanCentricPeakCharacterization")
## End(Not run)
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