Package 'chromConverter' reference manual

Title:	Chromatographic File Converter
Description:	Reads chromatograms from binary formats into R objects. Currently supports conversion of 'Agilent ChemStation', 'Agilent MassHunter', 'Shimadzu LabSolutions', 'ThermoRaw', and 'Varian Workstation' files as well as various text-based formats. In addition to its internal parsers, chromConverter contains bindings to parsers in external libraries, such as 'Aston' <https://github.com/bovee/aston>, 'Entab' <https://github.com/bovee/entab>, 'rainbow' <https://rainbow-api.readthedocs.io/>, and 'ThermoRawFileParser' <https://github.com/compomics/ThermoRawFileParser>.
Authors:	Ethan Bass [aut, cre] , James Dillon [ctb, cph] (Author and copyright holder of source code adapted from the 'Chromatography Toolbox' for parsing 'Agilent' FID files.), Evan Shi [ctb, cph] (Author and copyright holder of source code adapted from 'rainbow' for parsing 'Agilent' UV files.)
Maintainer:	Ethan Bass <[email protected]>
License:	GPL (>= 3)
Version:	0.7.1
Built:	2024-11-24 03:17:45 UTC
Source:	https://github.com/ethanbass/chromConverter

Call Entab Converts files using Entab parsers

Description

Call Entab Converts files using Entab parsers

Usage

call_entab(
  path,
  data_format = c("wide", "long"),
  format_out = c("matrix", "data.frame", "data.table"),
  format_in = "",
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
call_entab(
  path,
  data_format = c("wide", "long"),
  format_out = c("matrix", "data.frame", "data.table"),
  format_in = "",
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to file
`data_format`	Whether to return data in `wide` or `long` format.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`format_in`	Format of input.
`read_metadata`	Whether to read metadata from file.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Value

A chromatogram in the format specified by format_out (retention time x wavelength).

Parse files with OpenChrom

Description

Writes xml batch-files and calls OpenChrom file parsers using a system call to the command-line interface. To use this function OpenChrom (version 0.4.0) must be manually installed. The command line interface is no longer supported in the latest versions of OpenChrom (starting with version 0.5.0), so the function will no longer work with these newer versions. OpenChrom 1.4 has been scrubbed from the internet, but OpenChrom 1.3 is still available from SourceForge.

Usage

call_openchrom(
  files,
  path_out = NULL,
  format_in,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  export_format = c("mzml", "csv", "cdf", "animl"),
  return_paths = FALSE,
  verbose = getOption("verbose")
)
call_openchrom(
  files,
  path_out = NULL,
  format_in,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  export_format = c("mzml", "csv", "cdf", "animl"),
  return_paths = FALSE,
  verbose = getOption("verbose")
)

Arguments

`files`	files to parse
`path_out`	directory to export converted files.
`format_in`	Either `msd` for mass spectrometry data, `csd` for flame ionization data, or `wsd` for DAD/UV data.
`format_out`	R format. Either `matrix`, `data.frame` or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`export_format`	Either `mzml`, `csv`, `cdf`, `animl`. Defaults to `mzml`.
`return_paths`	Logical. If TRUE, the function will return a character vector of paths to the newly created files.
`verbose`	Logical. Whether to print output from OpenChrom to the console.

Details

The call_openchrom works by creating an xml batchfile and feeding it to the OpenChrom command-line interface. OpenChrom batchfiles consist of InputEntries (the files you want to convert) and ProcessEntries (what you want to do to the files). The parsers are organized into broad categories by detector-type and output format. The detector-types are msd (mass selective detectors), csd (current selective detectors, e.g. FID, ECD, NPD), and wsd (wavelength selective detectors, e.g. DAD, and UV/VIS). Thus, when calling the OpenChrom parsers, you must select one of these three options for the input format (format_in).

Value

If return_paths is FALSE, the function will return a list of chromatograms (if an appropriate parser is available to import the files into R). The chromatograms will be returned in matrix or data.frame format according to the value of format_out. If return_paths is TRUE, the function will return a character vector of paths to the newly created files.

Side effects

Chromatograms will be exported in the format specified by export_format in the folder specified by path_out.

Note

Activating the OpenChrom command-line will deactivate the graphical user interface (GUI). Thus, if you wish to continue using the OpenChrom GUI, it is recommended to create a separate command-line version of OpenChrom to call from R.

Author(s)

Ethan Bass

References

Wenig, Philip and Odermatt, Juergen. OpenChrom: A Cross-Platform Open Source Software for the Mass Spectrometric Analysis of Chromatographic Data. BMC Bioinformatics 11, no. 1 (July 30, 2010): 405. doi:10.1186/1471-2105-11-405.

Parse Agilent or Waters files with rainbow parser

Description

Uses rainbow parsers to read in Agilent (.D) and Waters (.raw) files. If format_in is agilent_d or waters_raw, a directory of the appropriate format (.d or .raw) should be provided to file. If format_in is chemstation_uv a .uv file should be provided. Data can be filtered by detector type using the what argument.

Usage

call_rainbow(
  path,
  format_in = c("agilent_d", "waters_raw", "masshunter", "chemstation", "chemstation_uv",
    "chemstation_fid"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  by = c("detector", "name"),
  what = NULL,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE,
  precision = 1
)
call_rainbow(
  path,
  format_in = c("agilent_d", "waters_raw", "masshunter", "chemstation", "chemstation_uv",
    "chemstation_fid"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  by = c("detector", "name"),
  what = NULL,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE,
  precision = 1
)

Arguments

`path`	Path to file
`format_in`	Format of the supplied files. Either `agilent_d`, `waters_raw`, or `chemstation`.
`format_out`	R format. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in wide or long format.
`by`	How to order the list that is returned. Either `detector` (default) or `name`.
`what`	What types of data to return (e.g. `MS`, `UV`, `CAD`, `ELSD`). This argument only applies if `by == "detector"`.
`read_metadata`	Logical. Whether to attach metadata. Defaults to TRUE.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`collapse`	Logical. Whether to collapse lists that only contain a single element.
`precision`	Number of decimals to round mz values. Defaults to 1.

Value

Returns a (nested) list of matrices or data.frames according to the value of format_out. Data is ordered according to the value of by.

Author(s)

Ethan Bass

Configure OpenChrom parser

Description

Configure OpenChrom parser

Usage

configure_openchrom(cli = c("null", "true", "false", "status"), path = NULL)
configure_openchrom(cli = c("null", "true", "false", "status"), path = NULL)

Arguments

`cli`	Defaults to NULL. If "true", R will rewrite openchrom ini file to enable CLI. If "false", R will disable CLI. If NULL, R will not modify the ini file.
`path`	Path to 'OpenChrom' executable (Optional). The supplied path will overwrite the current path.

Value

If cli is set to "status", returns a Boolean value indicating whether 'OpenChrom' is configured correctly. Otherwise, returns the path to OpenChrom command-line application.

Author(s)

Ethan Bass

Extract metadata

Description

Extract metadata as a data.frame from a list of chromatograms.

Usage

extract_metadata(
  chrom_list,
  what = c("instrument", "detector", "detector_id", "software", "method", "batch",
    "operator", "run_datetime", "sample_name", "sample_id", "injection_volume",
    "time_range", "time_interval", "time_unit", "detector_range", "detector_y_unit",
    "detector_x_unit", "intensity_multiplier", "scaled", "source_file",
    "source_file_format", "source_sha1", "data_format", "parser", "format_out"),
  format_out = c("data.frame", "tibble")
)
extract_metadata(
  chrom_list,
  what = c("instrument", "detector", "detector_id", "software", "method", "batch",
    "operator", "run_datetime", "sample_name", "sample_id", "injection_volume",
    "time_range", "time_interval", "time_unit", "detector_range", "detector_y_unit",
    "detector_x_unit", "intensity_multiplier", "scaled", "source_file",
    "source_file_format", "source_sha1", "data_format", "parser", "format_out"),
  format_out = c("data.frame", "tibble")
)

Arguments

`chrom_list`	A list of chromatograms with attached metadata (as returned by `read_chroms` with `read_metadata = TRUE`).
`what`	A character vector specifying the metadata elements to extract.
`format_out`	Format of object. Either `data.frame` or `tibble`.

Value

A data.frame or tibble (according to the value of format_out), with samples as rows and the specified metadata elements as columns.

Read files from 'ChemStation' .D directories

Description

Agilent .ch files come in several different varieties. This parser can automatically detect and read several versions of these files from 'Agilent ChemStation' and 'Agilent OpenLab', including versions 30 and 130, which are generally produced by ultraviolet detectors, as well as 81, 179, and 181 which are generally produced by flame ionization (FID) detectors.

Usage

read_agilent_d(
  path,
  what = c("chroms", "dad", "peak_table"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)
read_agilent_d(
  path,
  what = c("chroms", "dad", "peak_table"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

`path`	Path to `.ch` file
`what`	Whether to extract chromatograms (`chroms`), DAD data (`dad`) and/or peak tables `peak_table`. Accepts multiple arguments. `ms_spectra`. Accepts multiple arguments.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`collapse`	Logical. Whether to collapse lists that only contain a single element.

Value

A list of chromatograms in the format specified by data_format and #' format_out. If data_format is wide, the chromatograms will be returned with retention times as rows and columns containing signal intensity for each signal. If long format is requested, retention times will be in the first column. The format_out argument determines whether the chromatogram is returned as a matrix, data.frame or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Author(s)

Ethan Bass

Parser for reading Agilent ('.dx') files into R

Description

Parser for reading Agilent ('.dx') files into R

Usage

read_agilent_dx(
  path,
  path_out = NULL,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE
)
read_agilent_dx(
  path,
  path_out = NULL,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE
)

Arguments

`path`	Path to `.dx` file.
`path_out`	Path to directory to export unzipped files.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Logical. Whether to attach metadata.

Value

A chromatogram in the format specified by format_out (retention time x wavelength).

Author(s)

Ethan Bass

Read Allotrope Simple Model (ASM) 2D chromatograms

Description

A parser for reading 'Allotrope Simple Model' files into R.

Usage

read_asm(
  path,
  data_format = c("wide", "long"),
  format_out = c("matrix", "data.frame", "data.table"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)
read_asm(
  path,
  data_format = c("wide", "long"),
  format_out = c("matrix", "data.frame", "data.table"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

`path`	Path to ASM `.json` file.
`data_format`	Whether to return data in `wide` or `long` format.
`format_out`	Matrix or data.frame.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`collapse`	Logical. Whether to collapse lists that only contain a single element. Defaults to `TRUE`.

Value

A 2D chromatogram in the format specified by data_format and format_out. If data_format is wide, the chromatogram will be returned with retention times as rows and a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether the chromatogram is returned as a matrix or data.frame. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Author(s)

Ethan Bass

Read CDF file

Description

Parser for Analytical Data Interchange (ANDI) netCDF files.

Usage

read_cdf(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  what = NULL,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE,
  ...
)
read_cdf(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  what = NULL,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE,
  ...
)

Arguments

`path`	Path to ANDI netCDF file.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format. For 2D files, "long" format returns the retention time as the first column of the data.frame or matrix while "wide" format returns the retention time as the rownames of the object.
`what`	For ANDI chrom files, whether to extract `chroms` and/or `peak_table`. For ANDI ms files, whether to extract MS1 scans (`MS1`) or the total ion chromatogram (`TIC`).
`read_metadata`	Whether to read metadata from file.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`collapse`	Logical. Whether to collapse lists that only contain a single element.
`...`	Additional arguments to parser. The `ms_format` argument can be used here to specify whether to return mass spectra in `list` format or as a `data.frame`.

Value

A chromatogram in the format specified by the format_out and data_format arguments.

Author(s)

Ethan Bass

Read 'ChemStation' CH files

Description

Usage

read_chemstation_ch(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE
)
read_chemstation_ch(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE
)

Arguments

`path`	Path to `.ch` file
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`scale`	Whether to scale the data by the scaling factor present in the file. Defaults to `TRUE`. 'MassHunter' seems to ignore the scaling factor in at least some types of 'ChemStation' files.

Value

A 2D chromatogram in the format specified by data_format and format_out. If data_format is wide, the chromatogram will be returned with retention times as rows and a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether the chromatogram is returned as a matrix, data.frame, or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Note

This function was adapted from the Chromatography Toolbox (&copy James Dillon 2014).

Author(s)

Ethan Bass

Read Chemstation CSV

Description

Reads 'Agilent Chemstation' CSV files into R.

Usage

read_chemstation_csv(
  path,
  format_out = c("matrix", "data.frame", "data.table")
)
read_chemstation_csv(
  path,
  format_out = c("matrix", "data.frame", "data.table")
)

Arguments

`path`	Path to file
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.

Details

'Agilent Chemstation' CSV files are encoded in UTF-16.

Value

A chromatogram in the format specified by format_out (retention time x wavelength).

Author(s)

Ethan Bass

Read 'Agilent ChemStation' MS file.

Description

Parser to read Agilent Chemstation 'MSD Spectral Files' beginning with x01/x32/x00/x00.

Usage

read_chemstation_ms(
  path,
  what = c("MS1", "BPC", "TIC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)
read_chemstation_ms(
  path,
  what = c("MS1", "BPC", "TIC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

`path`	Path to `.ms` file
`what`	What stream to get: current options are `MS1`, `BPC` and/or `TIC`. If a stream is not specified, the function will return all streams.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`collapse`	Logical. Whether to collapse lists that only contain a single element. Defaults to `TRUE`.

Value

A 2D chromatogram in the format specified by data_format and format_out. If data_format is wide, the chromatogram will be returned with retention times as rows and a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether the chromatogram is returned as a matrix, data.frame, or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Note

Many thanks to Evan Shi and Eugene Kwan for providing helpful information on the structure of these files in the rainbow documentation.

Author(s)

Ethan Bass

Read 'Agilent ChemStation' Reports

Description

Read 'Agilent ChemStation' Reports

Usage

read_chemstation_reports(
  paths,
  data_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw")
)
read_chemstation_reports(
  paths,
  data_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw")
)

Arguments

`paths`	Paths to 'ChemStation' report files.
`data_format`	Format to output data. Either `chromatographr` or `chemstation`.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Value

A data.frame containing the information from the specified 'ChemStation' report.

Author(s)

Ethan Bass

Read 'ChemStation' DAD files

Description

Agilent .uv files come in several different varieties. This parser can automatically detect and read several versions of these files from 'Agilent ChemStation' and 'Agilent OpenLab', including versions 31 and 131.

Usage

read_chemstation_uv(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE
)
read_chemstation_uv(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE
)

Arguments

`path`	Path to `.uv` file.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`scale`	Whether to scale the data by the scaling factor present in the file. Defaults to `TRUE`.

Value

A 3D chromatogram in the format specified by data_format and format_out. If data_format is wide, the chromatogram will be returned with retention times as rows and wavelengths as columns. If long format is requested, three columns will be returned: one for the retention time, one for the wavelength and one for the intensity. The format_out argument determines whether the chromatogram is returned as a matrix or data.frame. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Note

This function was adapted from the parser in the rainbow project licensed under GPL 3 by Evan Shi https://rainbow-api.readthedocs.io/en/latest/agilent/uv.html.

Author(s)

Ethan Bass

Chromeleon ASCII reader

Description

Reads 'Thermo Fisher Chromeleon™ CDS' files into R.

Usage

read_chromeleon(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
read_chromeleon(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to file
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Whether to read metadata from file.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Value

A chromatogram in the format specified by format_out. (retention time x wavelength).

Author(s)

Ethan Bass

Read Chromatograms

Description

Reads chromatograms from specified folders or vector of paths using either an internal parser or bindings to an external library, such as Aston, Entab, ThermoRawFileParser, OpenChrom, rainbow.

Usage

read_chroms(
  paths,
  format_in = c("agilent_d", "agilent_dx", "asm", "chemstation", "chemstation_fid",
    "chemstation_ch", "chemstation_csv", "chemstation_ms", "chemstation_uv",
    "masshunter_dad", "chromeleon_uv", "mzml", "mzxml", "mdf", "shimadzu_ascii",
    "shimadzu_dad", "shimadzu_fid", "shimadzu_gcd", "shimadzu_qgd", "shimadzu_lcd",
    "thermoraw", "varian_sms", "waters_arw", "waters_raw", "msd", "csd", "wsd", "other"),
  find_files,
  pattern = NULL,
  parser = c("", "chromconverter", "aston", "entab", "thermoraw", "openchrom", "rainbow"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  path_out = NULL,
  export_format = c("", "csv", "chemstation_csv", "cdf", "mzml", "animl"),
  force = FALSE,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  progress_bar,
  cl = 1,
  verbose = getOption("verbose"),
  sample_names = NULL,
  dat = NULL,
  ...
)
read_chroms(
  paths,
  format_in = c("agilent_d", "agilent_dx", "asm", "chemstation", "chemstation_fid",
    "chemstation_ch", "chemstation_csv", "chemstation_ms", "chemstation_uv",
    "masshunter_dad", "chromeleon_uv", "mzml", "mzxml", "mdf", "shimadzu_ascii",
    "shimadzu_dad", "shimadzu_fid", "shimadzu_gcd", "shimadzu_qgd", "shimadzu_lcd",
    "thermoraw", "varian_sms", "waters_arw", "waters_raw", "msd", "csd", "wsd", "other"),
  find_files,
  pattern = NULL,
  parser = c("", "chromconverter", "aston", "entab", "thermoraw", "openchrom", "rainbow"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  path_out = NULL,
  export_format = c("", "csv", "chemstation_csv", "cdf", "mzml", "animl"),
  force = FALSE,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  progress_bar,
  cl = 1,
  verbose = getOption("verbose"),
  sample_names = NULL,
  dat = NULL,
  ...
)

Arguments

`paths`	Paths to data files or directories containing the files.
`format_in`	Format of files to be imported/converted. Current options include: `agilent_d`, `agilent_dx`, `chemstation`, `chemstation_uv`, `chemstation_ch`, `chemstation_csv`, `chemstation_ms`, `masshunter`, `masshunter_dad`, `chromeleon_uv`, `shimadzu_ascii`, `shimadzu_fid`, `shimadzu_dad`, `thermoraw`, `waters_arw`, `waters_raw`, `mzml`, `mzxml`, `cdf`, `mdf`, `msd`, `csd`, `wsd`, or `other`.
`find_files`	Logical. Set to `TRUE` (default) if you are providing the function with a folder or vector of folders containing the files. Otherwise, set to`FALSE`.
`pattern`	pattern (e.g. a file extension). Defaults to NULL, in which case file extension will be deduced from `format_in`.
`parser`	What parser to use (optional). Current option are `chromconverter`, `aston`, `entab`, `thermoraw`, `openchrom`, or `rainbow`.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to output data in wide or long format. Either `wide` or `long`.
`path_out`	Path for exporting files. If path not specified, files will export to current working directory.
`export_format`	Export format. Currently the options include `.csv`, `chemstation_csv` (utf-16 encoding), and `cdf`, unless you are using OpenChrom parsers, where there are two additional options: `mzml`, and `animl`.
`force`	Logical. Whether to overwrite files when exporting. Defaults to `FALSE`.
`read_metadata`	Logical, whether to attach metadata (if it's available). Defaults to TRUE.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`progress_bar`	Logical. Whether to show progress bar. Defaults to `TRUE` if `pbapply` is installed.
`cl`	Argument to `pbapply` specifying the number of clusters to use or a cluster object created by `makeCluster`. Defaults to 1.
`verbose`	Logical. Whether to print output from external parsers to the R console.
`sample_names`	An optional character vector of sample names. Otherwise sample names default to the `basename` of the specified files.
`dat`	Existing list of chromatograms to append results. (Defaults to NULL).
`...`	Additional arguments to parser.

Details

Provides a unified interface to all chromConverter parsers. Currently recognizes 'Agilent ChemStation' (.uv, .ch, .dx), 'Agilent MassHunter' (.dad), 'Thermo RAW' (.raw), 'Waters ARW' (.arw), 'Waters RAW' (.raw), 'Chromeleon ASCII' (.txt), 'Shimadzu ASCII' (.txt), 'Shimadzu GCD', 'Shimadzu LCD' (DAD and chromatogram streams) and 'Shimadzu QGD' files. Also, wraps 'OpenChrom' parsers, which include many additional formats. To use 'Entab', 'ThermoRawFileParser', or 'OpenChrom' parsers, they must be manually installed. Please see the instructions in the README for further details.

If paths to individual files are provided, read_chroms will try to infer the file format and select an appropriate parser. However, when providing paths to directories, the file format must be specified using the format_in argument.

Value

A list of chromatograms in matrix, data.frame, or data.table format, according to the value of format_out. Chromatograms may be returned in either wide or long format according to the value of data_format.

Side effects

If an export_format is provided, chromatograms will be exported in the specified format specified into the folder specified by path_out. Files can currently be converted to csv, mzml, or cdf format. If an openchrom parser is selected, ANIML is available as an additional option.

Author(s)

Ethan Bass

Examples


path <- "tests/testthat/testdata/dad1.uv"
chr <- read_chroms(path, find_files = FALSE, format_in = "chemstation_uv")

path <- "tests/testthat/testdata/dad1.uv"
chr <- read_chroms(path, find_files = FALSE, format_in = "chemstation_uv")

Read 'Lumex' MDF files into R

Description

Read 'Lumex' MDF files into R

Usage

read_mdf(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE
)
read_mdf(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE
)

Arguments

`path`	The path to a 'Lumex' `.mdf` file.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Whether to read metadata from file.

Value

A chromatogram in the format specified by the format_out and data_format arguments (retention time x wavelength).

Author(s)

Ethan Bass

Extract data from mzML files

Description

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,
  ...
)
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(s)

Ethan Bass

Read peak lists

Description

Reads peak lists from specified folders or vector of paths.

Usage

read_peaklist(
  paths,
  find_files,
  format_in = c("chemstation", "shimadzu_fid", "shimadzu_dad"),
  pattern = NULL,
  data_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw"),
  read_metadata = TRUE,
  progress_bar,
  cl = 1
)
read_peaklist(
  paths,
  find_files,
  format_in = c("chemstation", "shimadzu_fid", "shimadzu_dad"),
  pattern = NULL,
  data_format = c("chromatographr", "original"),
  metadata_format = c("chromconverter", "raw"),
  read_metadata = TRUE,
  progress_bar,
  cl = 1
)

Arguments

`paths`	paths to files or folders containing files.
`find_files`	Logical. Set to `TRUE` (default) if you are providing the function with a folder or vector of folders containing the files. Otherwise, set to`FALSE`.
`format_in`	Format of files to be imported/converted. Current options include: `chemstation` or `shimadzu`.
`pattern`	pattern (e.g. a file extension). Defaults to NULL, in which case file extension will be deduced from `format_in`.
`data_format`	Either `chromatographr` or `original`.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`read_metadata`	Logical, whether to attach metadata (if it's available). Defaults to TRUE.
`progress_bar`	Logical. Whether to show progress bar. Defaults to `TRUE` if `pbapply` is installed.
`cl`	Argument to `pbapply` specifying the number of clusters to use or a cluster object created by `makeCluster`. Defaults to 1.

Value

A list of chromatograms in matrix or data.frame format, according to the value of format_out.

Author(s)

Ethan Bass

Examples


path <- "tests/testthat/testdata/dad1.uv"
chr <- read_chroms(path, find_files = FALSE, format_in = "chemstation_uv")

path <- "tests/testthat/testdata/dad1.uv"
chr <- read_chroms(path, find_files = FALSE, format_in = "chemstation_uv")

Shimadzu ascii reader

Description

Reads 'Shimadzu' ascii files into R. These files can be exported from 'Shimadzu LabSolutions' by right clicking on samples in the sample list and selecting File Conversion:Convert to ASCII.

Usage

read_shimadzu(
  path,
  what = "chroms",
  format_in = NULL,
  include = c("fid", "lc", "dad", "uv", "tic"),
  format_out = c("matrix", "data.frame"),
  data_format = c("wide", "long"),
  peaktable_format = c("chromatographr", "original"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  ms_format = c("data.frame", "list"),
  collapse = TRUE,
  scale = TRUE
)
read_shimadzu(
  path,
  what = "chroms",
  format_in = NULL,
  include = c("fid", "lc", "dad", "uv", "tic"),
  format_out = c("matrix", "data.frame"),
  data_format = c("wide", "long"),
  peaktable_format = c("chromatographr", "original"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  ms_format = c("data.frame", "list"),
  collapse = TRUE,
  scale = TRUE
)

Arguments

`path`	Path to file.
`what`	Whether to extract chromatograms (`chroms`), `peak_table`, and/or `ms_spectra`. Accepts multiple arguments.
`format_in`	This argument is deprecated and is no longer required.
`include`	Which chromatograms to include. Options are `fid`, `dad`, `uv`, `tic`, and `status`.
`format_out`	R format. Either `matrix` or `data.frame`.
`data_format`	Whether to return data in `wide` or `long` format.
`peaktable_format`	Whether to return peak tables in `chromatographr` or `original` format.
`read_metadata`	Whether to read metadata from file.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`ms_format`	Whether to return mass spectral data as a (long) `data.frame` or a `list`.
`collapse`	Logical. Whether to collapse lists that only contain a single element.
`scale`	Whether to scale the data by the scaling factor present in the file. Defaults to `TRUE`.

Value

A nested list of elements from the specified file, where the top levels are chromatograms, peak tables, and/or mass spectra according to the value of what. Chromatograms are returned in the format specified by format_out (retention time x wavelength).

Author(s)

Ethan Bass

Shimadzu GCD parser

Description

Read chromatogram data streams from 'Shimadzu' GCD files.

Usage

read_shimadzu_gcd(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
read_shimadzu_gcd(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to GCD file.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Details

A parser to read chromatogram data streams from 'Shimadzu' .gcd files. GCD files are encoded as 'Microsoft' OLE documents. The parser relies on the olefile package in Python to unpack the files. The PDA data is encoded in a stream called PDA 3D Raw Data:3D Raw Data. The GCD data stream contains a segment for each retention time, beginning with a 24-byte header.

The 24 byte header consists of the following fields:

4 bytes: segment label (17234).
4 bytes: Little-endian integer specifying the sampling interval in milliseconds.
4 bytes: Little-endian integer specifying the number of values in the file.
4 bytes: Little-endian integer specifying the total number of bytes in the file (However, this seems to be off by a few bytes?).
8 bytes of 00s

After the header, the data are simply encoded as 64-bit (little-endian) floating-point numbers. The retention times can be (approximately?) derived from the number of values and the sampling interval encoded in the header.

Value

A 2D chromatogram from the chromatogram stream in matrix or data.frame format, according to the value of format_out. The chromatograms will be returned in wide or long format according to the value of data_format.

Note

This parser is experimental and may still need some work. It is not yet able to interpret much metadata from the files.

Author(s)

Ethan Bass

Shimadzu LCD parser

Description

Read 3D PDA or 2D chromatogram streams from 'Shimadzu' LCD files.

Usage

read_shimadzu_lcd(
  path,
  what,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE,
  collapse = TRUE
)
read_shimadzu_lcd(
  path,
  what,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  scale = TRUE,
  collapse = TRUE
)

Arguments

`path`	Path to LCD file.
`what`	What stream to get: current options are `pda`, chromatograms `chroms`, or `tic`. If a stream is not specified, the function will default to `pda` if the PDA stream is present.
`format_out`	Matrix or data.frame.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`scale`	Whether to scale the data by the value factor. Defaults to `TRUE`.
`collapse`	Logical. Whether to collapse lists that only contain a single element.

Details

A parser to read data from 'Shimadzu' .lcd files. LCD files are encoded as 'Microsoft' OLE documents. The parser relies on the olefile package in Python to unpack the files. The PDA data is encoded in a stream called PDA 3D Raw Data:3D Raw Data. The PDA data stream contains a segment for each retention time, beginning with a 24-byte header.

The 24 byte header consists of the following fields:

4 bytes: segment label (17234).
4 bytes: Little-endian integer specifying the sampling rate along the time axis for 2D streams or along the spectral axis (?) for PDA streams.
4 bytes: Little-endian integer specifying the number of values in the file (for 2D data) or the number of wavelength values in each segment (for 3D data).
4 bytes: Little-endian integer specifying the total number of bytes in the segment.
8 bytes of 00.

For 3D data, Each time point is divided into two sub-segments, which begin and end with an integer specifying the length of the sub-segment in bytes. 2D data are structured similarly but with more segments. All known values in this the LCD data streams are little-endian and the data are delta-encoded. The first hexadecimal digit of each value is a sign digit specifying the number of bytes in the delta and whether the value is positive or negative. The sign digit represents the number of hexadecimal digits used to encode each value. Even numbered sign digits correspond to positive deltas, whereas odd numbers indicate negative deltas. Positive values are encoded as little-endian integers, while negative values are encoded as two's complements. The value at each position is derived by subtracting the delta at each position from the previous value.

Value

A chromatogram or list of chromatograms in the format specified by data_format and format_out. If data_format is wide, the chromatogram(s) will be returned with retention times as rows and a single column for the intensity. If long format is requested, two columns will be returned: one for the retention time and one for the intensity. The format_out argument determines whether chromatograms are returned as a matrix, data.frame, or data.table. Metadata can be attached to the chromatogram as attributes if read_metadata is TRUE.

Note

My parsing of the date-time format seems to be a little off, since the acquisition times diverge slightly from the ASCII file.

Author(s)

Ethan Bass

Read 'Shimadzu' QGD

Description

Parser for 'Shimadzu GCMSsolution' .qgd files.

Usage

read_shimadzu_qgd(
  path,
  what = c("MS1", "TIC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)
read_shimadzu_qgd(
  path,
  what = c("MS1", "TIC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

`path`	Path to 'Shimadzu' QGD file.
`what`	What stream to get: current options are `MS1` and/or `TIC`. If a stream is not specified, the function will return both streams.
`format_out`	Matrix or data.frame.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`collapse`	Logical. Whether to collapse lists that only contain a single element. Defaults to `TRUE`.

Details

The MS data is stored in the "GCMS Raw Data" storage, which contains a MS Raw Data stream with MS scans, a TIC Data stream containing the total ion chromatogram, and a Retention Time stream containing the retention times. All known values are little-endian. The retention time stream is a simple array of 4-byte integers. The TIC stream is a simple array of 8-byte integers corresponding to retention times stored in the retention time stream. The MS Raw Data stream is blocked by retention time. Each block begins with a header consisting of the following elements:

scan number (4-byte integer)
retention time (4-byte integer)
unknown (12-bytes)
number of bytes in intensity values (2-byte integer)
unknown (8-bytes)

After the header, the rest of the block consists of an array of mz values and intensities. The mz values are encoded as 2-byte integers where each mz value is scaled by a factor of 20. Intensities are encoded as (unsigned) integers with variable byte-length defined by the value in the header.

Value

A 2D chromatogram from the chromatogram stream in matrix, data.frame, or data.table format, according to the value of format_out. The chromatograms will be returned in wide or long format according to the value of data_format.

Note

This parser is experimental and may still need some work. It is not yet able to interpret much metadata from the files.

Author(s)

Ethan Bass

Shimadzu LCD 2D parser

Description

Read 2D PDA data stream from 'Shimadzu' LCD files.

Usage

read_sz_lcd_2d(
  path,
  format_out = "data.frame",
  data_format = "wide",
  read_metadata = TRUE,
  metadata_format = "shimadzu_lcd",
  scale = TRUE
)
read_sz_lcd_2d(
  path,
  format_out = "data.frame",
  data_format = "wide",
  read_metadata = TRUE,
  metadata_format = "shimadzu_lcd",
  scale = TRUE
)

Arguments

`path`	Path to LCD file.
`format_out`	Matrix or data.frame.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`scale`	Whether to scale the data by the value factor.

Details

A parser to read chromatogram data streams from 'Shimadzu' .lcd files. LCD files are encoded as 'Microsoft' OLE documents. The parser relies on the olefile package in Python to unpack the files. The chromatogram data is encoded in streams titled LSS Raw Data:Chromatogram Ch<#>. The chromatogram data streams begin with a 24-byte header.

The 24 byte header consists of the following fields:

4 bytes: segment label (17234).
4 bytes: Little-endian integer specifying the sampling rate (in milliseconds).
4 bytes: Little-endian integer specifying the number of values in the file.
4 bytes: Little-endian integer specifying the total number of bytes in the file.
8 bytes of 00s

Each segment is divided into multiple sub-segments, which begin and end with an integer specifying the length of the sub-segment in bytes. All known values in this data stream are little-endian and the data are delta-encoded. The first hexadecimal digit of each value is a sign digit specifying the number of bytes in the delta and whether the value is positive or negative. The sign digit represents the number of hexadecimal digits used to encode each value. Even numbered sign digits correspond to positive deltas, whereas odd numbers indicate negative deltas. Positive values are encoded as little-endian integers, while negative values are encoded as two's complements. The value at each position is derived by subtracting the delta at each position from the previous value.

Value

One or more 2D chromatograms from the chromatogram streams in matrix or data.frame format, according to the value of format_out. If multiple chromatograms are found, they will be returned as a list of matrices or data.frames. The chromatograms will be returned in wide or long format according to the value of data_format.

Author(s)

Ethan Bass

Shimadzu LCD 3D parser

Description

Read 3D PDA data stream from 'Shimadzu' LCD files.

Usage

read_sz_lcd_3d(
  path,
  format_out = "matrix",
  data_format = "wide",
  read_metadata = TRUE,
  metadata_format = "shimadzu_lcd",
  scale = TRUE
)
read_sz_lcd_3d(
  path,
  format_out = "matrix",
  data_format = "wide",
  read_metadata = TRUE,
  metadata_format = "shimadzu_lcd",
  scale = TRUE
)

Arguments

`path`	Path to LCD file.
`format_out`	Matrix or data.frame.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`scale`	Whether to scale the data by the value factor.

Details

A parser to read PDA data from 'Shimadzu' .lcd files. LCD files are encoded as 'Microsoft' OLE documents. The parser relies on the olefile package in Python to unpack the files. The PDA data is encoded in a stream called PDA 3D Raw Data:3D Raw Data. The PDA data stream contains a segment for each retention time, beginning with a 24-byte header.

The 24 byte header consists of the following fields:

4 bytes: segment label (17234).
4 bytes: Little-endian integer specifying the wavelength bandwidth (?).
4 bytes: Little-endian integer specifying the number of wavelength values in the segment.
4 bytes: Little-endian integer specifying the total number of bytes in the segment.
8 bytes of 00s

Each segment is divided into two sub-segments, which begin and end with an integer specifying the length of the sub-segment in bytes. All known values in this data stream are little-endian and the data are delta-encoded. The first hexadecimal digit of each value is a sign digit specifying the number of bytes in the delta and whether the value is positive or negative. The sign digit represents the number of hexadecimal digits used to encode each value. Even numbered sign digits correspond to positive deltas, whereas odd numbers indicate negative deltas. Positive values are encoded as little-endian integers, while negative values are encoded as two's complements. The value at each position is derived by subtracting the delta at each position from the previous value.

Value

A 3D chromatogram from the PDA stream in matrix or data.frame format, according to the value of format_out. The chromatograms will be returned in wide or long format according to the value of data_format.

Author(s)

Ethan Bass

Read ThermoRaw files into R using ThermoRawFileParser

Description

Converts ThermoRawFiles to mzML by calling the ThermoRawFileParser from the command-line.

Usage

read_thermoraw(
  path,
  path_out = NULL,
  format_out = c("matrix", "data.frame"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  verbose = getOption("verbose")
)
read_thermoraw(
  path,
  path_out = NULL,
  format_out = c("matrix", "data.frame"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  verbose = getOption("verbose")
)

Arguments

`path`	Path to file.
`path_out`	Path to directory to export `mzML` files. If `path_out` isn't specified, a temp directory will be used.
`format_out`	R format. Either `matrix` or `data.frame`.
`read_metadata`	Whether to read metadata from file.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.
`verbose`	Logical. Whether to print output from OpenChrom to the console.

Details

To use this function, the ThermoRawFileParser must be manually installed.

Value

A chromatogram in the format specified by format_out.

Side effects

Exports chromatograms in mzML format to the folder specified by path_out.

Author(s)

Ethan Bass

References

Hulstaert Niels, Jim Shofstahl, Timo Sachsenberg, Mathias Walzer, Harald Barsnes, Lennart Martens, and Yasset Perez-Riverol. ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion. Journal of Proteome Research 19, no. 1 (January 3, 2020): 537–42. doi:10.1021/acs.jproteome.9b00328.

Examples

## Not run: 
read_thermoraw(path)

## End(Not run)
## Not run: 
read_thermoraw(path)

## End(Not run)

Read 'Varian' peaklist. Read peak list(s) from 'Varian MS Workstation'.

Description

Read 'Varian' peaklist. Read peak list(s) from 'Varian MS Workstation'.

Usage

read_varian_peaklist(path)
read_varian_peaklist(path)

Arguments

path

Path to Varian peak list file.

Value

A data.frame containing the information from the specified report.

Author(s)

Ethan Bass

Read 'Varian' SMS

Description

Parser for reading 'Varian Workstation' SMS file.

Usage

read_varian_sms(
  path,
  what = c("MS1", "TIC", "BPC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  collapse = TRUE
)
read_varian_sms(
  path,
  what = c("MS1", "TIC", "BPC"),
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  collapse = TRUE
)

Arguments

`path`	Path to `.SMS` files.
`what`	Whether to extract chromatograms (`chroms`) and/or `MS1` data. Accepts multiple arguments.
`format_out`	R format. Either `matrix` or `data.frame`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Whether to read metadata from file. (This is just a placeholder for now as there is not yet support for parsing metadata).
`collapse`	Logical. Whether to collapse lists that only contain a single element.

Details

Varian SMS files begin with a "DIRECTORY" with offsets for each section. The first section (in all the files I've been able to inspect) is "MSData" generally beginning at byte 3238. This MSdata section is in turn divided into two sections. The first section (after a short header) contains chromatogram data. Some of the information found in this section includes scan numbers, retention times, (as 64-bit floats), the total ion chromatogram (TIC), the base peak chromatogram (BPC), ion time (µsec), as well as some other unidentified information. The scan numbers and intensities for the TIC and BPC are stored at 4-byte little-endian integers. Following this section, there is a series of null bytes, followed by a series of segments containing the mass spectra.

The encoding scheme for the mass spectra is somewhat more complicated. Each scan is represented by a series of values of variable length separated from the next scan by two null bytes. Within these segments, values are paired. The first value in each pair represents the delta-encoded mass-to-charge ratio, while the second value represents the intensity of the signal. Values in this section are variable-length, big-endian integers that are encoded using a selective bit masking based on the leading digit (d) of each value. The length of each integer seems to be determined as 1 + (d %/% 4). Integers beginning with digits 0-3 are simple 2-byte integers. If d >= 4, values are determined by masking to preserve the lowest n bits according to the following scheme:

d = 4-5 -> preserve lowest 13 bits
d = 6-7 -> preserve lowest 14 bits
d = 8-9 -> preserve lowest 21 bits
d = 10-11 (A-B) -> preserve lowest 22 bits
d = 12-13 (C-D) -> preserve lowest 27 bits
d = 14-15 (E-F) -> preserve lowest 28 bits (?)

Value

A chromatogram or list of chromatograms from the specified file, according to the value of what. Chromatograms are returned in the format specified by format_out.

Note

There is still only limited support for the extraction of metadata from this file format. Also, the timestamp conversions aren't quite right.

Author(s)

Ethan Bass

Waters ascii (.arw) reader

Description

Reads 'Waters ARW' files.

Usage

read_waters_arw(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
read_waters_arw(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to file
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Whether to read metadata from file.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Details

For help exporting files from Empower, you can consult the official documentation: How_to_export_3D_raw_data_from_Empower.

Value

A chromatogram in the format specified by format_out (retention time x wavelength).

Author(s)

Ethan Bass

Read 'Waters' RAW

Description

Parser for reading 'Waters MassLynx (.raw) files into R.

Usage

read_waters_raw(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
read_waters_raw(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to `.raw` file.
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Either `wide` (default) or `long`.
`read_metadata`	Logical. Whether to attach metadata.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Value

A chromatogram in the format specified by format_out (retention time x wavelength).

Note

For now this parser only reads 1D chromatograms (not mass spectra or DAD data) and does not support parsing of metadata from 'Waters' RAW files.

Author(s)

Ethan Bass

Converter for 'Agilent MassHunter' UV files

Description

Converts a single chromatogram from MassHunter .sp format to R data.frame.

Usage

sp_converter(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
sp_converter(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to file
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`read_metadata`	Logical. Whether to read metadata and attach it to the chromatogram.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Details

Uses the Aston file parser.

Value

A chromatogram in data.frame format (retention time x wavelength).

Converter for 'Agilent ChemStation' UV files

Description

Converts a single chromatogram from ChemStation .uv format to R data.frame.

Usage

uv_converter(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  correction = TRUE,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)
uv_converter(
  path,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  correction = TRUE,
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw")
)

Arguments

`path`	Path to file
`format_out`	Class of output. Either `matrix`, `data.frame`, or `data.table`.
`data_format`	Whether to return data in `wide` or `long` format.
`correction`	Logical. Whether to apply empirical correction. Defaults is TRUE.
`read_metadata`	Logical. Whether to read metadata and attach it to the chromatogram.
`metadata_format`	Format to output metadata. Either `chromconverter` or `raw`.

Details

Uses the Aston file parser.

Value

A chromatogram in data.frame format (retention time x wavelength).

Write ANDI chrom CDF file from chromatogram

Description

Exports a chromatogram in ANDI (Analytical Data Interchange) chromatography format (ASTM E1947-98). This format can only accommodate unidimensional data. For two-dimensional chromatograms, the column to export can be specified using the lambda argument. Otherwise, a warning will be generated and the first column of the chromatogram will be exported.

Usage

write_andi_chrom(x, path_out, sample_name = NULL, lambda = NULL, force = FALSE)
write_andi_chrom(x, path_out, sample_name = NULL, lambda = NULL, force = FALSE)

Arguments

`x`	A chromatogram in (wide) format.
`path_out`	The path to write the file.
`sample_name`	The name of the file. If a name is not provided, the name will be derived from the `sample_name` attribute.
`lambda`	The wavelength to export (for 2-dimensional chromatograms). Must be a string matching one the columns in `x` or the index of the column to export.
`force`	Whether to overwrite existing files at the specified path. Defaults to `FALSE`.

Value

No return value. The function is called for its side effects.

Side effects

Exports a chromatogram in ANDI chromatography format (netCDF) in the directory specified by path_out. The file will be named according to the value of sample_name. If no sample_name is provided, the sample_name attribute will be used if it exists.

Author(s)

Ethan Bass

Export chromatograms

Description

Export chromatograms

Usage

write_chroms(
  chrom_list,
  path_out,
  export_format = c("mzml", "cdf", "csv"),
  what = "",
  force = FALSE,
  show_progress = TRUE,
  verbose = getOption("verbose"),
  ...
)
write_chroms(
  chrom_list,
  path_out,
  export_format = c("mzml", "cdf", "csv"),
  what = "",
  force = FALSE,
  show_progress = TRUE,
  verbose = getOption("verbose"),
  ...
)

Arguments

`chrom_list`	A list of chromatograms.
`path_out`	Path to directory for writing files.
`export_format`	Format to export files: either `mzml`, `cdf`, or `csv`.
`what`	What to write. Either `MS1` or `chrom`.
`force`	Logical. Whether to overwrite existing files. Defaults to `TRUE`.
`show_progress`	Logical. Whether to show progress bar. Defaults to `TRUE`.
`verbose`	Logical. Whether to print verbose output.
`...`	Additional arguments to write function.

Author(s)

Ethan Bass

Write mzML

Description

This function constructs mzML files using a streaming XML-writing approach, generating and writing XML content directly to a file connection. This method is memory-efficient and fast, making it well-suited for large mzML files. However, it may be less flexible than DOM-based methods for handling complex XML structures or large-scale modifications after writing has begun.

Usage

write_mzml(
  data,
  path_out,
  sample_name = NULL,
  what = NULL,
  instrument_info = NULL,
  compress = TRUE,
  indexed = TRUE,
  force = FALSE,
  show_progress = TRUE,
  verbose = getOption("verbose")
)
write_mzml(
  data,
  path_out,
  sample_name = NULL,
  what = NULL,
  instrument_info = NULL,
  compress = TRUE,
  indexed = TRUE,
  force = FALSE,
  show_progress = TRUE,
  verbose = getOption("verbose")
)

Arguments

`data`	List of data.frames or data.tables containing spectral data.
`path_out`	The path to write the file.
`sample_name`	The name of the file. If a name is not provided, the name will be derived from the `sample_name` attribute.
`what`	Which streams to write to mzML: `"ms1"`, `"ms2"`, `"tic"`, `"bpc"`, and/or `"dad"`.
`instrument_info`	Instrument info to write to mzML file.
`compress`	Logical. Whether to use zlib compression. Defaults to `TRUE`.
`indexed`	Logical. Whether to write indexed mzML. Defaults to `TRUE`.
`force`	Logical. Whether to overwrite existing files at `path_out`. Defaults to `FALSE`.
`show_progress`	Logical. Whether to show progress bar. Defaults to `TRUE`.
`verbose`	Logical. Whether or not to print status messages.

Details

This function constructs mzML files by writing XML strings directly to a file connection. While this approach is memory-efficient and fast, it may be less flexible for handling complex XML structures.

The function supports writing various types of spectral data including MS1, MS2, TIC (Total Ion Current), BPC (Base Peak Chromatogram), and DAD (Diode Array Detector) data.

If indexed = TRUE, the function will create an indexed mzML file, which allows faster random access to spectra.

Value

Invisibly returns the path to the written mzML file.

Author(s)

Ethan Bass

Package 'chromConverter'

Help Index

Call Entab Converts files using Entab parsers

Description

Usage

Arguments

Value

Parse files with OpenChrom

Description

Usage

Arguments

Details

Value

Side effects

Note

Author(s)

References

Parse Agilent or Waters files with rainbow parser

Description

Usage

Arguments

Value

Author(s)

Configure OpenChrom parser

Description

Usage

Arguments

Value

Author(s)

Extract metadata

Description

Usage

Arguments

Value

Read files from 'ChemStation' .D directories

Description

Usage

Arguments

Value

Author(s)

Parser for reading Agilent ('.dx') files into R

Description

Usage

Arguments

Value

Author(s)

Read Allotrope Simple Model (ASM) 2D chromatograms

Description

Usage

Arguments

Value

Author(s)

Read CDF file

Description

Usage

Arguments

Value

Author(s)

Read 'ChemStation' CH files

Description

Usage

Arguments

Value

Note

Author(s)

Read Chemstation CSV

Description

Usage

Arguments

Details

Value

Author(s)

Read 'Agilent ChemStation' MS file.

Description

Usage

Arguments

Value

Note

Author(s)

Read 'Agilent ChemStation' Reports