In ChemoSpec, spectral data sets are stored in an S3 class called Spectra, which contains a variety of information in addition to the spectra themselves. Spectra objects are created by files2SpectraObject or matrix2SpectraObject.


The structure of a Spectra object is a list of 9 elements and an attribute as follows:

  • $freq (numeric) A common frequency (or wavelength) axis for all the spectra.

  • $data (numeric) The intensities for the spectra. A matrix of dimension no. samples x no. frequency points.

  • $names (character) The sample names for the spectra; length must be no. samples.

  • $groups (factor) The group classification of the samples; length must be no. samples.

  • $colors (character) The colors for each sample; length must be no. samples. Groups and colors correspond.

  • $sym (integer) As for colors, but symbols for plotting (if b/w is desired).

  • $alt.sym (character) Lower-case letters as alternate symbols for plotting.

  • $unit (character) Two entries, the first giving the x axis unit, the second the y axis unit.

  • $desc (character) A character string describing the data set. This appears on plots and therefore should probably be kept to 40 characters or less.

  • attribute: character with value "Spectra" The S3 class designation.

See also

sumSpectra to summarize a Spectra object. sumGroups to summarize group membership of a Spectra object. chkSpectra to verify the integrity of a Spectra object. colorSymbol for a discussion of color options. Finally, additional documentation at


Bryan A. Hanson (DePauw University).