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.
Bryan A. Hanson, DePauw University.
#> List of 8 #> $ F2 : num [1:100] 0 0.0505 0.101 0.1515 0.202 ... #> $ F1 : num [1:50] 10 11.4 12.9 14.3 15.7 ... #> $ data :List of 10 #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> ..$ : num [1:50, 1:100] 0.08046 0.03152 0.05684 0.00853 0.00185 ... #> $ names : chr [1:10] "Alcohol_1" "Alcohol_2" "Alcohol_3" "Alcohol_4" ... #> $ groups: Factor w/ 2 levels "Alcohol","Ether": 1 1 1 1 1 2 2 2 2 2 #> $ colors: chr [1:10] "black" "black" "black" "black" ... #> $ units : expression(""^1 * H ~ ppm, ""^13 * C ~ ppm, "intensity") #> $ desc : chr "MUD1: HSQC-like data for testing. See ?MUD1" #> - attr(*, "class")= chr "Spectra2D"#> #> MUD1: HSQC-like data for testing. See ?MUD1 #> #> There are 10 spectra in this set. #> #> The F2 dimension runs from 0 to 5 ""^1 * H ~ ppm #> and there are 100 data points. #> #> The F1 dimension runs from 10 to 80 ""^13 * C ~ ppm #> and there are 50 slices. #> #> The spectra are divided into 2 groups: #> #> group no. color #> 1 Alcohol 5 black #> 2 Ether 5 red #> #> *** Note: this is an S3 object #> of class 'Spectra2D'