lcms_read_samples: Read mzXML samples
In sipss/AlpsLCMS: Signal processing of LC-MS metabolomics

Description Usage Arguments Value See Also Examples

Read LCMS samples on mzXML format.

1	lcms_read_samples(...)

...

Arguments passed on to MSnbase::readMSData

files: A character with file names to be read and parsed.
pdata: An object of class AnnotatedDataFrame or NULL (default).
msLevel.: MS level spectra to be read. In inMemory mode, use 1 for MS1 spectra or any larger numeric for MSn spectra. Default is 2 for InMemory mode. onDisk mode supports multiple levels and will, by default, read all the data.
verbose: Verbosity flag. Default is to use isMSnbaseVerbose().
centroided.: A logical, indicating whether spectra are centroided or not. Default is NA in which case the information is extracted from the raw file (for mzML or mzXML files). In onDisk, it can also be set for different MS levels by a vector of logicals, where the first element is for MS1, the second element is for MS2, ... See OnDiskMSnExp for an example.
smoothed.: A logical indicating whether spectra already smoothed or not. Default is NA.
cache.: Numeric indicating caching level. Default is 0 for MS1 and 1 MS2 (or higher). Only relevant for inMemory mode.
mode: On of "inMemory" (default) or "onDisk". The former loads the raw data in memory, while the latter only generates the object and the raw data is accessed on disk when needed. See the benchmarking vignette for memory and speed implications.

A lcms_dataset.

Other import/export functions: lcms_convert_ipo_to_xcms(), lcms_dataset_load(), lcms_dataset_save(), lcms_identify_metabolites(), lcms_meta_export(), lcms_meta_read(), lcms_peak_annotation(), lcms_raw_data(), lcms_read_ipo_to_xcms(), lcms_rearrange_datafiles_by_class(), lcms_sig_peaks_table(), lcms_spectral_sig_features(), lcms_to_mait(), lcms_write_opt_params(), lcms_write_parameter_table(), phData()

## Not run: 
file_path <- system.file("extdata", package = "AlpsLCMS")
rawconverter <- NULL
file_format <- "mzXML"
samples_mzxml <- lcms_list_mzxml_samples(file_path,
                                        file_format = file_format,
                                        rawconverter = rawconverter)
samples_mzxml <- as.character(samples_mzxml)
dataset <- suppressWarnings(lcms_read_samples(samples_mzxml, mode = "onDisk"))

print(dataset)

## End(Not run)