read_chroms {chromConverter} | R Documentation |
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")