chromConverter aims to facilitate the conversion of chromatography data from various proprietary formats so it can be easily read into R for further analysis. It currently consists of wrappers around file parsers from various external libraries including Aston, Entab, the ThermoRawFileParser, and OpenChrom as well as some parsers written natively in R for various text-based formats.
.sp).raw).gcd, .C0#).raw).run).PRM)*.mfg).wiff).txt).mzml).txt).arw) (provisional support)chromConverter can now be installed directly from CRAN:
install.packages("chromConverter")Alternatively, the development version of chromConverter can be installed from GitHub as follows:
install.packages("devtools")
devtools::install_github("https://github.com/ethanbass/chromConverter/")Some of the parsers rely on external software libraries that must be manually installed.
To install Aston, call the configure_aston() function to
install miniconda along with the necessary python dependencies. Running
read_chroms with the Aston parser selected should also
trigger a prompt to install Aston. If you’re running Windows, you may
need to install the latest version of ‘Microsoft
Visual C++’ if you don’t already have it.
Entab is a Rust-based parsing framework for converting a variety of scientific file formats into tabular data. To use parsers from Entab, you must first install Rust and Entab-R. After following the instructions to install Rust, you can install Entab from GitHub as follows:
devtools::install_github("https://github.com/bovee/entab/", subdir = "entab-r")Thermo RAW files can be converted by calling the ThermoRawFileParser on the command-line. To install the ThermoRawFileParser, follow the instructions here. If you are running Linux or Mac OS X, you will also need to install mono, following the instructions provided at the link. In addition, when you use chromConverter to convert Thermo RAW files for the first time you will be asked to enter the path to the program.
OpenChrom is opensource chromatography software, containing a large number of file parsers, which can now be conveniently accessed directly from R. Strangely, configuring OpenChrom for use on the command-line deactivates the graphical user interface (GUI). Thus, it is recommended to make a separate copy of OpenChrom if you’d still like to access the GUI. To use the OpenChrom parsers, follow the steps detailed below:
configure_openchrom_parser(cli="true") or by calling the
openchrom_parser and following the prompts.read_chroms with parser="openchrom".
The first time you call the parser, it will ask you to provide the path
to your local installation of OpenChrom. The path will then be saved for
future use. If the command-line interface is disabled, you will be given
the option to automatically activate the command-line.read_chromes functionThe workhorse of chromConverter is the read_chroms
function, which functions as a wrapper around all of the supported
parsers. To convert files, call read_chroms, specifying the
paths to a vector of directories or files and the
appropriate file format (format_in). The supported formats
include chemstation_uv, chemstation_csv,
masshunter_dad, shimadzu_fid,
shimadzu_dad, chromeleon_uv,
thermoraw, mzml, waters_arw,
msd, csd, and wsd.
library(chromConverter)
dat <- read_chroms(path, format.in = "chemstation_uv")The read_chroms function will attempt to determine an
appropriate parser to use and whether you’ve provided a vector of
directories or files. However, if you’d like to be more explicit, you
can provide input to the parsers and
find_files arguments. Setting
find_files = FALSE will instruct the function that you are
providing a vector of files, while find_files = TRUE
implies that you are providing a vector of directories.
If you’d like to automatically export the files, include the argument
export=TRUE along with the path where you’d like to export
the files (path_out). Some parsers
(e.g. OpenChrom and ThermoRawFileParser) need
to export files for their basic operations. Thus, if these parsers are
selected, you will need to specify an argument to
path_out.
library(chromConverter)
dat <- read_chroms(path, find_files = FALSE, path_out="temp", export=TRUE)For formats where multiple parsers are available, you can choose
between them using the parser argument. For example,
Agilent files can be read using either the Aston or Entab parsers (or in
some cases OpenChrom). In this case, it is recommended to use the newer
Entab parsers, since Aston is no longer actively supported. However
Entab is slightly more complicated to install (see installation instructions above).
Parsers in OpenChrom are organized by detector-type. Thus, for the
format_in argument, the user must specify whether the files
come from a mass selective detector (msd), a
current-selective detector like a flame-ionization detector
(csd), or a wavelength-selective detector
(wsd), rather than providing a specific file format. In
addition, the user should specify what format they’d like to export
(export_format). Current options include csv,
cdf, mzml, or animl (the
analytical information markup language). The files will then be
converted by calling OpenChrom through the command-line interface. If
the files are exported in csv format, the chromatograms
will be automatically read into R. Otherwise, files will be exported to
the specified folder but will not be read into the R workspace.
chromConverter includes some options to extract metadata from the
provided files. If read_metadata=TRUE, metadata will be
extracted and stored as attributes of the associated
object. A list of attributes
can be extracted from any R object using the attributes()
function.
For downstream analyses of chromatographic data, you can also check out my package chromatographR. For interactive visualization of chromatograms, you can check out my new package ShinyChromViewer (alpha release).