Read 'Allotrope Simple Model' (ASM) files

Reads chromatograms, mass spectra and peak lists from 'Allotrope Simple Model' chromatography files into R.

Usage

read_asm(
  path,
  what = c("chroms", "MS1"),
  data_format = c("wide", "long"),
  format_out = c("matrix", "data.frame", "data.table"),
  peaktable_format = c("chromatographr", "original"),
  read_metadata = TRUE,
  metadata_format = c("chromconverter", "raw"),
  collapse = TRUE
)

Arguments

path

Path to ASM .json file.

what

What to read: 2D chromatograms (chroms), mass spectra (MS1), peak lists (peak_table) and/or instrument traces (instrument), such as pump pressure, flow rate or temperature. Defaults to chroms and MS1, dropping whichever the file does not contain.

data_format

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

format_out

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

peaktable_format

Whether to return peak tables in chromatographr format (rt, start, end, area and height) or original format, with every field the file records under its ASM name.

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.

Value

A 2D chromatogram in the format specified by format_out and data_format, or a list of them named by detection type if the file holds more than one (or collapse = FALSE). Mass spectra are returned as a data.frame (or data.table) with columns rt, mz and intensity, and peak tables as a data.frame (or data.table) per measurement. Instrument traces are returned as 2D chromatograms named by trace. Where more than one of these is returned, they are combined in a list named by what. A file with several injections returns a chrom_list with one such element per injection. Metadata are attached as attributes if read_metadata is TRUE.

Details

Retention times are returned in the unit the file declares, which is recorded in the time_unit attribute.

A file can hold several injections, such as a sequence exported from a chromatography data system. Each injection is then returned as a separate sample, named by its sample name, and read_chroms adds each one to the list of samples it returns.

Mass spectra have so far only been tested against the example files published by the Allotrope Foundation.

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_asm("path/to/file.json")
read_asm("path/to/file.json", what = "peak_table")
} # }