Read 'Chromatotec' file

Reads 'Chromatotec' .Chrom files.

Usage

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

Arguments

path

The path to 'Chromatotec' .Chrom file.

what

Whether to extract chromatograms (chrom) and/or peak_table data. Accepts multiple arguments, and defaults to both.

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.

peaktable_format

Whether to return peak tables in the standard chromatographr layout (the default) or with all the columns the file provides (original). A chromatographr table has the columns rt, start, end, area, height and FWHM (the full width at half maximum), with times in the same unit as the format's chromatograms and NA where the file does not record a value.

Value

A chromatogram and/or peak table from the specified path, according to the value of what, with times in minutes. Chromatograms are returned in the format specified by format_out. The rows of the peak table that report a total over most of the run rather than a peak, such as NMTHC-EqC6 and THC_PAMS, are only kept with peaktable_format = "original". In the original table, Start and End are where integration of the peak starts and ends, and SubstanceIndex appears to be the position of its substance in the run's substance table (0 for an unnamed peak); U1, U3 and U4 have not been identified.

Author

Ethan Bass

Examples

if (FALSE) { # \dontrun{
read_chromatotec(path)
} # }