Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.
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Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.
library(Spectra)
library(MsBackendMassbank)
fls <- dir(system.file("extdata", package = "MsBackendMassbank"), full.names = TRUE, pattern = "txt$")
sps <- Spectra(fls, source = MsBackendMassbank(), backend = MsBackendDataFrame(), nonStop = TRUE)
sps <- dropNaSpectraVariables(sps)
Input: A character vector of paths to MassBank text files. Output: A Spectra object containing the imported mass spectrometry data.
Spectra objects.MsBackendMassbankSql.compareSpectra and plotSpectraMirror.xcms.Spectra backends like MsBackendMzR.MsBackendMassbank() or MsBackendMassbankSql() specifying the data source.MsBackendDataFrame() or other Spectra backends to store the imported data.TRUE, prevents the import from stopping when problematic MassBank files are encountered.metaDataBlocks(ac = TRUE, ms = TRUE).compareSpectra or plotSpectraMirror.nonStop = TRUE when importing a large number of MassBank files to prevent a single malformed file from crashing the process.dropNaSpectraVariables to remove imported spectra variables that contain only missing values across all spectra.MsBackendMassbankSql for large-scale analyses to fetch data on demand from a local SQL database instead of loading thousands of text files into memory.MsBackendMassbankSql: The database connection cannot be shared across parallel processes, so parallel processing is silently disabled.metaDataBlocks or use the SQL backend.Spectra with MsBackendDataFrame for in-memory generic spectrum handling.MsCoreUtils for low-level mass spectrometry helper functions.No reviews yet. Tell others what you thought.
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