Extract data from mzML files — read

Extracts data from mzML files using parsers from either RaMS or mzR. The RaMS parser (default) will only return data in tidy (long) format. The mzR parser will return data in wide format. Currently the mzR-based parser is configured to return only DAD data.

Usage

read_mzml(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("long", "wide"),
  parser = c("RaMS", "mzR"),
  what = c("MS1", "MS2", "BPC", "TIC", "DAD", "chroms", "metadata", "everything"),
  verbose = FALSE,
  ...
)

Arguments

path: path to file
format_out: Class of output. Only applies if mzR is selected. Either matrix, data.frame, or data.table. RaMS will return a list of data.tables regardless of what is selected here.
data_format: Whether to return data in wide or long format.
parser: What parser to use. Either RaMS or mzR.
what: What types of data to return (argument to grabMSdata. Options include MS1, MS2, BPC, TIC, DAD, chroms, metadata, or everything).
verbose: Argument to grabMSdata controlling verbosity.
...: Additional arguments to grabMSdata.

Value

If RaMS is selected, the function will return a list of "tidy" data.table objects. If mzR is selected, the function will return a chromatogram in matrix or data.frame format according to the value of format_out.

Author

Ethan Bass