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Read files from 'Agilent' .rslt directories

Source: R/read_agilent_rslt.R
read_agilent_rslt.Rd

Reads a sequence of injections from an 'Agilent' .rslt directory. Combines raw chromatogram data from .dx files with injection-level metadata parsed from the accompanying .acaml file.

Usage

read_agilent_rslt(
  path,
  what = c("chroms", "dad"),
  path_out = NULL,
  format_out = c("matrix", "data.frame", "data.table"),
  data_format = c("wide", "long"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE,
  sample_names = c("basename", "sample_name"),
  progress_bar = FALSE,
  cl = 1
)

Arguments

path

Path to 'Agilent' .rslt directory.

what

Whether to extract chromatograms (chroms), DAD data (dad) and/or auxiliary instrumental data (instrument) (e.g., temperature, pressure, solvent composition, etc.). Accepts multiple arguments.

path_out

A directory to export unzipped files. If a path is not specified, the files will be written to a temp directory on the disk. The function will overwrite existing folders in the specified directory that share the basename of the file specified by path.

format_out

Class of output. Either matrix, data.frame, or data.table.

data_format

Whether to return data in wide (default) or long format.

read_metadata

Logical. Whether to attach metadata. Defaults to TRUE.

metadata_format

Format to output metadata. Either chromconverter (standardized field names) or raw (vendor field names, unmapped).

collapse

Logical. Whether to collapse lists that only contain a single element. Defaults to TRUE.

sample_names

How to name the chromatograms that are returned. Either basename (default), to use the name of the source .dx file, or sample_name, to use the sample name field from the metadata.

progress_bar

Logical. Whether to show a progress bar while reading the sequence's .dx files. Defaults to FALSE, since read_chroms already reports progress over the directories it found and a second bar inside each one would be redrawn per directory. Set to TRUE when calling this function directly on a sequence with many injections.

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 (one read_agilent_dx-style result per injection in the sequence), in the format specified by data_format and format_out. If read_metadata is TRUE, injection-level metadata parsed from the .acaml file is attached to each chromatogram as an attribute.

Details

Currently this function only reads .dx chromatogram files. Peak tables stored in .rx files are not yet supported.

See also

Other 'Agilent' parsers: read_agilent_d(), read_agilent_dx(), read_chemstation_ch(), read_chemstation_csv(), read_chemstation_ms(), read_chemstation_reports(), read_chemstation_uv()

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_agilent_rslt("path/to/sequence.rslt")
} # }