| Title: | Chromatographic File Converter |
| Version: | 0.7.5 |
| Maintainer: | Ethan Bass <ethanbass@gmail.com> |
| 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. |
| License: | GPL (≥ 3) |
| URL: | https://ethanbass.github.io/chromConverter/, https://github.com/ethanbass/chromConverter/ |
| BugReports: | https://github.com/ethanbass/chromConverter/issues/ |
| Depends: | R (≥ 4.1.0) |
| Imports: | bitops, fs, purrr, readxl, reticulate (≥ 1.41.0), stringr, tidyr, utils, RaMS, tibble, xml2, bit64, data.table, base64enc, jsonlite, digest |
| Suggests: | entab, ncdf4, pbapply, testthat (≥ 3.0.0), mzR, chromConverterExtraTests |
| Encoding: | UTF-8 |
| Language: | en-US |
| RoxygenNote: | 7.3.2.9000 |
| Additional_repositories: | https://ethanbass.github.io/drat/, https://ethanbass.r-universe.dev/ |
| Config/testthat/edition: | 3 |
| Config/Needs/website: | rmarkdown, ggplot2, dplyr |
| NeedsCompilation: | no |
| Packaged: | 2025-03-30 21:04:36 UTC; ethanbass |
| Author: | 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.) |
| Repository: | CRAN |
| Date/Publication: | 2025-03-31 19:10:02 UTC |
Call Entab
Description
Converts chromatography date 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")
)
Arguments
path |
Path to file. |
data_format |
Whether to return data in |
format_out |
Class of output. Either |
format_in |
Format of input. |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
Value
A chromatogram in the format specified by format_out
(retention time x wavelength).
See Also
Other external parsers:
call_openchrom(),
call_rainbow(),
read_thermoraw(),
sp_converter(),
uv_converter()
Parse files with OpenChrom
Description
Writes xml batch-files and calls OpenChrom file parsers using a
system call to the command-line interface. Unfortunately, the command-line
interface is no longer supported in newer versions of OpenChrom (starting with
version 1.5.0) and older versions of OpenChrom that do support
the command line interface are no longer available from Lablicate. Thus, this
function is deprecated since it will only work if you happen to have access
to OpenChrom version 1.4.0, which has been scrubbed from the internet.
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")
)
Arguments
files |
Path to files. |
path_out |
Directory to export converted files. |
format_in |
Either |
format_out |
R format. Either |
data_format |
Whether to return data in |
export_format |
Either |
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 function 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.
See Also
Other external parsers:
call_entab(),
call_rainbow(),
read_thermoraw(),
sp_converter(),
uv_converter()
Call 'rainbow' parsers Parse 'Agilent' or 'Waters' files with rainbow parsers
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 the file argument. 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
)
Arguments
path |
Path to file. |
format_in |
Format of the supplied files. Either |
format_out |
R format. Either |
data_format |
Whether to return data in wide or long format. |
by |
How to order the list that is returned. Either |
what |
What types of data to return (e.g. |
read_metadata |
Logical. Whether to attach metadata. Defaults to TRUE. |
metadata_format |
Format to output metadata. Either |
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
See Also
Other external parsers:
call_entab(),
call_openchrom(),
read_thermoraw(),
sp_converter(),
uv_converter()
Configure 'OpenChrom' parser
Description
Configures OpenChrom to use command-line interface. Requires OpenChrom version prior to 0.5.0.
Usage
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
See Also
Configure python environment
Description
Configures reticulate environment for parsers that have python dependencies.
Deprecated as this should no longer be necessary with reticulate v1.41.0.
Usage
configure_python_environment(parser = "all", return_boolean = FALSE)
Arguments
parser |
Either |
return_boolean |
Logical. Whether to return a Boolean value indicating if the chromConverter environment is correctly configured. |
Value
If return_boolean is TRUE, returns a Boolean value
indicating whether the chromConverter environment is configured correctly.
Otherwise, there is no return value.
Author(s)
Ethan Bass
Extract metadata
Description
Extract metadata as a data.frame or tibble 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", "data.table", "tibble")
)
Arguments
chrom_list |
A list of chromatograms with attached metadata (as returned
by |
what |
A character vector specifying the metadata elements to extract. |
format_out |
Format of object. Either |
Value
A data.frame, tibble, or data.table (according
to the value of format_out), with samples as rows and the specified
metadata elements as columns.
Read files from 'Agilent ChemStation' .D directories
Description
Reads files from 'Agilent' .D directories.
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
)
Arguments
path |
Path to 'Agilent' |
what |
Whether to extract chromatograms ( |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Logical. Whether to attach metadata. |
metadata_format |
Format to output metadata. Either |
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
See Also
Other 'Agilent' parsers:
read_agilent_dx(),
read_chemstation_ch(),
read_chemstation_csv(),
read_chemstation_ms(),
read_chemstation_reports(),
read_chemstation_uv()
Examples
read_agilent_d("tests/testthat/testdata/RUTIN2.D")
Read 'Agilent' DX files
Description
Reads 'Agilent' .dx files.
Usage
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 |
path_out |
Path to directory to export unzipped files. |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Logical. Whether to attach metadata. |
Details
This function unzips 'Agilent' .dx into a temporary directory using
unzip and calls read_chemstation_ch.
Value
A chromatogram in the format specified by format_out
(retention time x wavelength).
Author(s)
Ethan Bass
See Also
Other 'Agilent' parsers:
read_agilent_d(),
read_chemstation_ch(),
read_chemstation_csv(),
read_chemstation_ms(),
read_chemstation_reports(),
read_chemstation_uv()
Read 'Allotrope Simple Model' (ASM) 2D chromatograms
Description
Reads '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
)
Arguments
path |
Path to ASM |
data_format |
Whether to return data in |
format_out |
Matrix or data.frame. |
read_metadata |
Logical. Whether to attach metadata. |
metadata_format |
Format to output metadata. Either |
collapse |
Logical. Whether to collapse lists that only contain a single
element. Defaults to |
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
Description
Reads 'Analytical Data Interchange' (ANDI) netCDF (.cdf) 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,
...
)
Arguments
path |
Path to ANDI netCDF file. |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
what |
For ANDI chrom files, whether to extract |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
collapse |
Logical. Whether to collapse lists that only contain a single element. |
... |
Additional arguments to parser. The |
Value
A chromatogram in the format specified by the format_out and
data_format arguments.
Author(s)
Ethan Bass
Read 'Agilent ChemStation' CH files
Description
Reads 'Agilent ChemStation' .ch files.
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
)
Arguments
path |
Path to 'Agilent' |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
scale |
Whether to scale the data by the scaling factor present in the
file. Defaults to |
Details
'Agilent' .ch files come in several different formats. 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.
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 (© James Dillon 2014).
Author(s)
Ethan Bass
See Also
Other 'Agilent' parsers:
read_agilent_d(),
read_agilent_dx(),
read_chemstation_csv(),
read_chemstation_ms(),
read_chemstation_reports(),
read_chemstation_uv()
Examples
read_chemstation_ch("tests/testthat/testdata/chemstation_130.ch")
Read 'Agilent ChemStation' CSV files
Description
Reads 'Agilent Chemstation' .csv files.
Usage
read_chemstation_csv(
path,
format_out = c("matrix", "data.frame", "data.table")
)
Arguments
path |
Path to 'Agilent' |
format_out |
Class of output. Either |
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
See Also
Other 'Agilent' parsers:
read_agilent_d(),
read_agilent_dx(),
read_chemstation_ch(),
read_chemstation_ms(),
read_chemstation_reports(),
read_chemstation_uv()
Examples
read_chemstation_csv("tests/testthat/testdata/dad1.csv")
Read 'Agilent ChemStation' MS file.
Description
Reads '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
)
Arguments
path |
Path to 'Agilent' |
what |
What stream to get: current options are |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
collapse |
Logical. Whether to collapse lists that only contain a single
element. Defaults to |
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
See Also
Other 'Agilent' parsers:
read_agilent_d(),
read_agilent_dx(),
read_chemstation_ch(),
read_chemstation_csv(),
read_chemstation_reports(),
read_chemstation_uv()
Examples
## Not run:
read_chemstation_ms(path)
## End(Not run)
Read 'Agilent ChemStation' report files.
Description
Reads 'Agilent ChemStation' reports into R.
Usage
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 |
metadata_format |
Format to output metadata. Either |
Value
A data.frame containing the information from the specified 'ChemStation' report.
Author(s)
Ethan Bass
See Also
Other 'Agilent' parsers:
read_agilent_d(),
read_agilent_dx(),
read_chemstation_ch(),
read_chemstation_csv(),
read_chemstation_ms(),
read_chemstation_uv()
Read 'Agilent ChemStation' DAD files
Description
Agilent .uv files come in several different formats. 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
)
Arguments
path |
Path to 'Agilent' |
format_out |
Class of output. Either |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
scale |
Whether to scale the data by the scaling factor present in the
file. Defaults to |
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
See Also
Other 'Agilent' parsers:
read_agilent_d(),
read_agilent_dx(),
read_chemstation_ch(),
read_chemstation_csv(),
read_chemstation_ms(),
read_chemstation_reports()
Examples
read_chemstation_uv("tests/testthat/testdata/dad1.uv")
Read 'Chromeleon' ASCII files
Description
Reads 'Thermo Fisher Chromeleon™ CDS' ASCII (.txt) files.
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"),
decimal_mark = NULL
)
Arguments
path |
Path to 'Chromeleon' ASCII file. |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
decimal_mark |
Which character is used as the decimal separator in the
file. By default, decimal mark will be detected automatically, but it can
also be manually set as |
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 = c("basename", "sample_name"),
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: |
find_files |
Logical. Set to |
pattern |
pattern (e.g. a file extension). Defaults to NULL, in which
case file extension will be deduced from |
parser |
What parser to use (optional). Current option are
|
format_out |
Class of output. Either |
data_format |
Whether to output data in wide or long format. Either
|
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 |
force |
Logical. Whether to overwrite files when exporting. Defaults to
|
read_metadata |
Logical, whether to attach metadata (if it's available). Defaults to TRUE. |
metadata_format |
Format to output metadata. Either |
progress_bar |
Logical. Whether to show progress bar. Defaults to
|
cl |
Argument to |
verbose |
Logical. Whether to print output from external parsers to the R console. |
sample_names |
Which sample names to use. Options are |
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")
Read 'Lumex' MDF
Description
Reads 'Lumex' .mdf files.
Usage
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' |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
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
Read 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,
...
)
Arguments
path |
Path to |
format_out |
Class of output. Only applies if |
data_format |
Whether to return data in |
parser |
What parser to use. Either |
what |
What types of data to return (argument to |
verbose |
Argument to |
... |
Additional arguments to |
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", "shimadzu_lcd",
"shimadzu_gcd"),
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 peak list files. |
find_files |
Logical. Set to |
format_in |
Format of files to be imported/converted. Current options
include: |
pattern |
pattern (e.g. a file extension). Defaults to NULL, in which
case file extension will be deduced from |
data_format |
Either |
metadata_format |
Format to output metadata. Either |
read_metadata |
Logical, whether to attach metadata (if it's available). Defaults to TRUE. |
progress_bar |
Logical. Whether to show progress bar. Defaults to
|
cl |
Argument to |
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")
Read 'Shimadzu' ASCII
Description
Reads 'Shimadzu' ASCII (.txt) files. 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
)
Arguments
path |
Path to Shimadzu |
what |
Whether to extract chromatograms ( |
format_in |
This argument is deprecated and is no longer required. |
include |
Which chromatograms to include. Options are |
format_out |
R format. Either |
data_format |
Whether to return data in |
peaktable_format |
Whether to return peak tables in |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
ms_format |
Whether to return mass spectral data as a (long)
|
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 |
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
See Also
Other 'Shimadzu' parsers:
read_shimadzu_gcd(),
read_shimadzu_lcd(),
read_shimadzu_qgd(),
read_sz_lcd_2d(),
read_sz_lcd_3d()
Examples
path <- "tests/testthat/testdata/ladder.txt"
read_shimadzu(path)
Read 'Shimadzu' GCD
Description
Read chromatogram data streams from 'Shimadzu' .gcd files.
Usage
read_shimadzu_gcd(
path,
what = "chroms",
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' |
what |
What stream to get: current options are chromatograms
( |
format_out |
Class of output. Either |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
collapse |
Logical. Whether to collapse lists that only contain a single element. |
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
See Also
Other 'Shimadzu' parsers:
read_shimadzu(),
read_shimadzu_lcd(),
read_shimadzu_qgd(),
read_sz_lcd_2d(),
read_sz_lcd_3d()
Read 'Shimadzu' LCD
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
)
Arguments
path |
Path to 'Shimadzu' |
what |
What stream to get: current options are |
format_out |
Matrix or data.frame. |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
scale |
Whether to scale the data by the value factor. Defaults to
|
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
See Also
Other 'Shimadzu' parsers:
read_shimadzu(),
read_shimadzu_gcd(),
read_shimadzu_qgd(),
read_sz_lcd_2d(),
read_sz_lcd_3d()
Examples
## Not run:
read_shimadzu_lcd(path)
## End(Not run)
Read 'Shimadzu' QGD files
Description
Reads 'Shimadzu GCMSsolution' .qgd GC-MS data 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
)
Arguments
path |
Path to 'Shimadzu' |
what |
What stream to get: current options are |
format_out |
Matrix or data.frame. |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. Defaults to |
metadata_format |
Format to output metadata. Either |
collapse |
Logical. Whether to collapse lists that only contain a single
element. Defaults to |
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.
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
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
See Also
Other 'Shimadzu' parsers:
read_shimadzu(),
read_shimadzu_gcd(),
read_shimadzu_lcd(),
read_sz_lcd_2d(),
read_sz_lcd_3d()
Read 'Shimadzu' LCD 2D data
Description
Reads 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
)
Arguments
path |
Path to 'Shimadzu' |
format_out |
Matrix or data.frame. |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. |
metadata_format |
Format to output metadata. Either |
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
See Also
Other 'Shimadzu' parsers:
read_shimadzu(),
read_shimadzu_gcd(),
read_shimadzu_lcd(),
read_shimadzu_qgd(),
read_sz_lcd_3d()
Read 'Shimadzu' LCD 3D data
Description
Reads 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
)
Arguments
path |
Path to 'Shimadzu' |
format_out |
Matrix or data.frame. |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. |
metadata_format |
Format to output metadata. Either |
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
See Also
Other 'Shimadzu' parsers:
read_shimadzu(),
read_shimadzu_gcd(),
read_shimadzu_lcd(),
read_shimadzu_qgd(),
read_sz_lcd_2d()
Read ThermoRaw
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")
)
Arguments
path |
Path to 'Thermo' |
path_out |
Path to directory to export |
format_out |
R format. Either |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
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.
See Also
Other external parsers:
call_entab(),
call_openchrom(),
call_rainbow(),
sp_converter(),
uv_converter()
Examples
## Not run:
read_thermoraw(path)
## End(Not run)
Read 'Varian' peak list.
Description
Read peak list(s) from 'Varian MS Workstation'.
Usage
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
See Also
Other 'Varian' parsers:
read_varian_sms()
Examples
## Not run:
read_varian_peaklist(path)
## End(Not run)
Read 'Varian' SMS
Description
Reads 'Varian Workstation' SMS files.
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
)
Arguments
path |
Path to 'Varian' |
what |
Whether to extract chromatograms ( |
format_out |
R format. Either |
data_format |
Whether to return data in |
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
See Also
Other 'Varian' parsers:
read_varian_peaklist()
Examples
## Not run:
read_varian_sms(path)
## End(Not run)
Read 'Waters' ASCII (.arw)
Description
Reads 'Waters' ASCII .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")
)
Arguments
path |
Path to Waters |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Whether to read metadata from file. |
metadata_format |
Format to output metadata. Either |
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
See Also
Other 'Waters' parsers:
read_waters_raw()
Read 'Waters' RAW
Description
Reads '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")
)
Arguments
path |
Path to Waters |
format_out |
Class of output. Either |
data_format |
Either |
read_metadata |
Logical. Whether to attach metadata. |
metadata_format |
Format to output metadata. Either |
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
See Also
Other 'Waters' parsers:
read_waters_arw()
Converter for 'Agilent MassHunter' UV files
Description
Converts a single chromatogram from MassHunter .sp format to R
data.frame using the Aston file parser.
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")
)
Arguments
path |
Path to file |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
read_metadata |
Logical. Whether to read metadata and attach it to the chromatogram. |
metadata_format |
Format to output metadata. Either |
Value
A chromatogram in data.frame format (retention time x wavelength).
See Also
Other external parsers:
call_entab(),
call_openchrom(),
call_rainbow(),
read_thermoraw(),
uv_converter()
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")
)
Arguments
path |
Path to file |
format_out |
Class of output. Either |
data_format |
Whether to return data in |
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 |
Details
Uses the Aston file parser.
Value
A chromatogram in data.frame format (retention time x wavelength).
See Also
Other external parsers:
call_entab(),
call_openchrom(),
call_rainbow(),
read_thermoraw(),
sp_converter()
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)
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 |
lambda |
The wavelength to export (for 2-dimensional chromatograms).
Must be a string matching one the columns in |
force |
Whether to overwrite existing files at the specified path.
Defaults to |
Value
Invisibly returns the path to the written CDF file.
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
See Also
Other write functions:
write_chroms(),
write_mzml()
Write chromatograms
Description
Writes chromatograms to disk in the format specified by export_format:
either (mzml), cdf or csv.
Usage
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 |
what |
What to write. Either |
force |
Logical. Whether to overwrite existing files. Defaults to |
show_progress |
Logical. Whether to show progress bar. Defaults to |
verbose |
Logical. Whether to print verbose output. |
... |
Additional arguments to write function. |
Value
No return value. The function is called for its side effects.
Side effects
Exports a chromatogram in the file format specified by export_format
in the directory specified by path_out.
Author(s)
Ethan Bass
See Also
Other write functions:
write_andi_chrom(),
write_mzml()
Write mzML
Description
This function constructs mzML files by writing XML strings directly to a file connection. While this approach is fast, it may be less flexible than methods based on an explicit Document Object Model (DOM).
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")
)
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 |
what |
Which streams to write to mzML: |
instrument_info |
Instrument info to write to mzML file. |
compress |
Logical. Whether to use zlib compression. Defaults to
|
indexed |
Logical. Whether to write indexed mzML. Defaults to
|
force |
Logical. Whether to overwrite existing files at |
show_progress |
Logical. Whether to show progress bar. Defaults to
|
verbose |
Logical. Whether or not to print status messages. |
Details
The function supports writing various types of spectral data including MS1, TIC (Total Ion Current), BPC (Base Peak Chromatogram), and DAD (Diode Array Detector) data. Support for MS2 may be added in a future release.
If indexed = TRUE, the function will generate 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
See Also
Other write functions:
write_andi_chrom(),
write_chroms()