sample_names argument in
read_chroms: This argument can no longer be
supplied with a vector of names. Instead, sample_names can
be provided with one of two arguments: basename or
sample_name. The default setting (basename)
will use the basename of the file, while sample_name will
instead use the sample name encoded in the file’s metadata.extract_metadata when sub-setting metadata
elements.extract_metadata.data.table format option to
extract_metadata.call_openchrom.call_openchrom
manual concerning OpenChrom installation.read_shimadzu_lcd to infer retention times in
Shimadzu 3D Data from Max Plot stream since it is always
(?) present.read_shimadzu_lcd to skip parsing of metadata
from 3D Data Item when it is not present.read_shimadzu_lcd to include
Max Plot stream when parsing 2D chromatograms.read_chromeleon related to inference of
decimal separators.decimal_mark argument to
read_chromeleon to manually set decimal separator..lcd files..lcd files lacking Data Item streams..lcd files..raw and Agilent .D)Waters chromatograms
with lowercase filenames..raw header files..sms) format through read_varian_sms
function.read_shimadzu_qgd function..D directories through read_agilent_d
function.read_agilent_ms.read_chroms so that
format_in comes second after path.export argument from
read_chroms. To export files, you now only need to provide
an argument to export_format.read_shimadzu_lcd. The function now returns a list of named
chromatograms if data_format == "wide" and returns multiple
chromatograms in a single data.frame if
data_format == "long".scale argument to
read_chemstation_uv and read_shimadzu_ascii to
toggle scaling of chromatograms.file arguments to path.read_cdf UI: what now
defaults to NULL and defaults are coded into downstream
read_andi_chrom and read_andi_ms
functions.read_chroms when
verbose is TRUE.reticulate::configure_environment).data.table as an option for
format_out.read_shimadzu_lcd by dealing with
twos-complements more sensibly.path_out when using
‘ThermoRawFileParser’ and ‘OpenChrom’ parsers.read_chroms if
path_out does not exist.mdf files lacking null bytes
after the file header.read_chroms.export_csv function to label first column for
wide-format chromatograms..ch)
files through read_chemstation_ch.Agilent Chemstation files due to typo.ChemStation CSV files
on (some) mac machines by specifying little-endian format in call to
read.csv.read_shimadzu_lcd_2d to more
accurately reflect file structure.scale argument to
read_chemstation_ch and read_shimadzu_lcd to
toggle scaling of chromatograms resolving (#30).read_shimadzu_lcd function to correctly
determine the number of blocks in the “Shimadzu” LCD PDA stream (thanks
to kco-hereon).export_cdfs function to permit
conversion of files lacking metadata..cdf) files.read_chemstation_ch parser to correctly read
“Mustang Chemstation” 179 files with 8-byte encoding.read_shimadzu function and added support
for new types of chromatograms (e.g. status, uv and total ion
chromatograms). Added support for reading multiple types of
chromatograms at once.read_shimadzu.write_cdf and added additional arguments
(lambda and force) for greater control by
users.read_waters_raw).collapse argument to call_rainbow
and to collapse superfluous lists.... argument to read_chroms for
supplying additional arguments to parsers.read_chroms for reading
mzxml files with RaMS.precision argument to call_rainbow
to control number of digits “mz” values are rounded to. (Also changed
default behavior so values are rounded to one decimal by default).read_shimadzu_lcd on Windows due to issue
with passing escaped paths to Python.pbapply
package. (Note: The pbapply package must
be manually installed to enable parallel processing).read_chemstation_uv function)..dx)
files (through read_agilentdx function)..lcd files through the
read_shimadzu_lcd function. Only the PDA stream (not MS) is
currently supported.read_peaklist function for reading peak lists.
Currently ‘Agilent ChemStation’ and ‘Shimadzu ASCII’ formats are
supported.verbose argument to control console output for
external parsers (‘OpenChrom’ and ‘ThermoRawFileParser’).read_chroms.read_thermoraw function to simplify
paths.thermoraw and openchrom parsers now
use a proper temp directory if an export directory is not specified
through the path_out argument.reshape_chroms, speeding up conversion from
wide to long format.openchrom export format to
mzml.what == "peak_table" and
read_metadata == TRUE).format_out == "matrix".data_format attributes in ‘Waters ARW’
and ‘Chromeleon’ parsers.chemstation_ch parser (version 130) (#17).arw) PDA
files..ch) files (version
30).read_chromeleon to better deal with comma
decimal separators in metadata.read_chromeleon to deal with more datetime
formats.read_chromeleon to deal with unicode
microliters.read_chemstation_ch.cdf files through the
read_cdf function..mdf files through the
read_mdf function.chemstation_csv (utf-16) and ANDI chrom cdf
files through read_chroms.read_chroms when providing direct paths to files (i.e. when
find_files == FALSE).read_varian_peaklist function for reading peak
lists from ‘Varian MS Workstation’.wide and long
data_format options for 2D data, such that the
wide format option writes retention times as rownames of
the matrix or data.frame. while the long format writes
retention times as the first column of the object.configure_openchrom for better discovery of
‘OpenChrom’ path and added path argument for directly
specifying the path to ‘OpenChrom’.source_file field to track data origin.fs package for parsing paths, eliminating buggy
check_paths function..uv) files
(version 131) through the read_chemstation_uv
function.extract_metadata function for extracting metadata
from a list of chromatograms and returning it as a
data.frame or tibble.progress_bar option in
read_chroms.reshape_chroms and reshape_chrom
to allow switching between “wide” and “long” formats.read_mzml.read_chroms.read_chroms.POSIXct
format..ch) files (version
130).read_chemstation_fid function to
read_chemstation_ch.read_chroms.format_data argument to
data_format to select wide or long format.mzML files with
RaMS..D) and “Waters”
(.raw) files with rainbow.data_format option available consistently for
choosing wide or long format..ch) data
(versions 81, 179 & 181).call_openchrom so that it can actually
find ‘OpenChrom’ path.call_openchrom to allow ‘animl’ as valid
export_format.configure_aston function for configuration of
Aston parsers and fixed issues with configuration of Aston.read_shimadzu function for parsing ‘Shimadzu’
ascii files.read_chromeleon function for parsing ‘Chromeleon’
ascii files.read_thermoraw function to convert ‘Thermo Raw’
files by calling the ‘ThermoRawFileParser’.read_mzml function to extract UV data from mzML
files using mzR.call_entab function for calling Entab
parsers.call_openchrom to call OpenChrom parsers through
the command-line interface.(All of the new functions described above can be called from the
read_chroms function by setting the format_in
and parser arguments).
read_metadata = TRUE in
read_chroms.read_chroms syntaxread_chroms will now automatically assign a parser if
the parser isn’t specified.read_chroms will throw more informative errors for
mismatch between format_in and parser
arguments.read_chroms will try to automatically determine if
files or directories are being provided.read_chroms syntax:Dots were replaced with underscores in all arguments to
read_chroms for internal syntactical consistency across the
package. Thus:
R.format to format_out.format.out to export_format.NEWS.md file to track changes to the
package.
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