SCZip: Represents the zip mass spec file
| SCZip | R Documentation |
Represents the zip mass spec file
Description
Represents the zip mass spec file
Represents the zip mass spec file
Details
This reference class represents the zip mass spec file. It does this by providing objects for the zip file, the metadata, as well as various bits underneath such as the mzml data and peak lists, and their associated metadata. Although it is possible to work with the SCZip object directly, it is heavily recommended to use the SCCharacterizePeaks object for carrying out the various steps of an analysis, including peak finding.
Public fields
zip_filethe actual zip file
zip_metadatathe metadata about the zip file
metadatathe metadata itself
metadata_filethe metadata file
sc_mzmlthe mzML data object.
peaks??
sc_peak_region_finderthe peak finder object
json_summaryjsonized summary of the peak characterization
idthe identifier of the sample
out_filewhere to put the final file
temp_directorywhere we keep everything until peak characterization is done
Methods
Public methods
Method load_mzml()
Loads the mzML file
Usage
SCZip$load_mzml()
Method load_sc_peak_region_finder()
Loads the SCPeakRegionFinder object
Usage
SCZip$load_sc_peak_region_finder()
Method save_json()
Save the jsonized summary out to actual json files
Usage
SCZip$save_json()
Method save_sc_peak_region_finder()
Saves the SCPeakRegionFinder binary object
Usage
SCZip$save_sc_peak_region_finder()
Method load_peak_list()
loads just the peak list data-frame instead of peak region finder
Usage
SCZip$load_peak_list()
Method compare_mzml_corresponded_densities()
compare peak densities
Usage
SCZip$compare_mzml_corresponded_densities( mz_range = c(150, 1600), window = 1, delta = 0.1 )
Arguments
mz_rangethe mz range to work over
windowthe window size in m/z
deltahow much to move the window
Method new()
Create a new SCZip object.
Usage
SCZip$new(
in_file,
mzml_meta_file = NULL,
out_file = NULL,
load_mzml = TRUE,
load_peak_list = TRUE,
temp_loc = tempfile("scpcms")
)Arguments
in_filethe mzML file to load
mzml_meta_filean optional metadata file
out_filewhere to save the final file
load_mzmlshould the mzML file actually be loaded into an SCMzml object?
load_peak_listshould the peak list be loaded if this is previously characterized?
temp_locwhere to make the temp file while working with the data
Method show_temp_dir()
Show the temp directory where everything is being worked with
Usage
SCZip$show_temp_dir()
Method write_zip()
Write the zip file
Usage
SCZip$write_zip(out_file = NULL)
Arguments
out_filewhere to save the zip file
Method cleanup()
delete the temp directory
Usage
SCZip$cleanup()
Method finalize()
delete when things are done
Usage
SCZip$finalize()
Method add_peak_list()
Add peak list data to the temp directory
Usage
SCZip$add_peak_list(peak_list_data)
Arguments
peak_list_datathe peak list data
Method clone()
The objects of this class are cloneable with this method.
Usage
SCZip$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
SCMzml
SCPeakRegionFinder
