In ChemoSpec2D
, spectral data sets are stored in an S3 class called
Spectra2D
, which contains a variety of information in addition to the
spectra themselves. Spectra2D
objects are created by
files2Spectra2DObject
.
The structure of a Spectra2D
object is a list of eight
elements and an attribute as follows:
w
element | type | description |
$F2 |
num | A common frequency (or wavelength) axis corresponding |
to the F2 dimension in NMR or the x axis more generally. | ||
Must be sorted ascending. | ||
$F1 |
num | A common frequency (or wavelength) axis corresponding |
to the F1 dimension in NMR or the y axis more generally. | ||
Must be sorted ascending. | ||
$data |
num | A list of matrices. Each matrix contains a 2D spectrum. |
Each matrix should have length(F1) rows and |
||
length(F2) columns. The matrix must not have dimnames. |
||
The low end of the F2 dimension is last column of the last row | ||
(lower right hand corner as typically displayed). The low end of | ||
the F1 dimension is the last column of the first row (upper right hand corner). | ||
In other words, the spectrum is stored as typically displayed. | ||
The list of matrices, if named, should have the same names as | ||
names . However, this is not currently enforced. |
||
$names |
chr | 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 | Colors for plotting; length must be no. samples. |
Colors correspond to groups. | ||
$units |
chr | Three entries, the first giving the F2 (x) axis unit, the |
second the F1 (y) axis unit, and the third the z axis unit, | ||
usually some kind of intensity. | ||
$desc |
chr | A character string describing the data set. |
- attr |
chr | "Spectra2D" The S3 class designation. |
sumSpectra
to summarize a Spectra2D
object.
sumGroups
to summarize group membership of a Spectra2D
object. chkSpectra
to verify the integrity of a
Spectra2D
object.
# NOT RUN {
data(MUD1)
str(MUD1)
sumSpectra(MUD1)
# }
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