feem | R Documentation |
Functions to create fluorescence excitation-emission matrix objects from
R matrices coupled with excitation and emission wavelengths, three-column
data.frame
s containing 3{
(\lambda_\mathrm{em}, \lambda_\mathrm{ex}, I)
feem(x, ...)
## S3 method for class 'matrix'
feem(x, emission, excitation, scale = 1, ...)
## S3 method for class 'data.frame'
feem(
x, scale = 1, emission = 'emission',
excitation = 'excitation', intensity = 'intensity', ...
)
## S3 method for class 'character'
feem(x, format, ...)
## S3 method for class 'connection'
feem(x, format, ...)
x |
The source of the information to create a FEEM object from: a matrix,
a three-column If converting a matrix, its rows should correspond to different
fluorescence emission wavelengths specified in the If converting a If reading a single file by file path or connection, the |
emission |
If converting a matrix, this should be a vector of emission wavelengths, each wavelength corresponding to a row of the matrix. If converting a |
excitation |
If converting a matrix, this should be a vector of excitation wavelengths, each wavelength corresponding to a column of the matrix. If converting a |
intensity |
If converting a |
scale |
The scale value of a EEM is preserved through the analysis procedure to divide the resulting score values after running PARAFAC. If the EEM has been pre-multiplied prior to creating the FEEM object, you can set the multiplier here. |
format |
Delta∆ exists where for all 3{ \lambda_\mathrm{em} - \lambda_\mathrm{ex} > \Delta lambda.em - lambda.ex > Delta λ<sub>em</sub> - λ<sub>ex</sub> > ∆ or 3{ \lambda_\mathrm{em} - \lambda_\mathrm{ex} < \Delta |
lambda.em - lambda.ex < Delta λ<sub>em</sub> - λ<sub>ex</sub> < ∆, 3{ X(\lambda_\mathrm{em}, \lambda_\mathrm{ex}) \in \mathtt{na}
Transposing a feem
object using t
will
remove the class attribute, returning an ordinary matrix.
A FEEM object is a matrix with the following attributes added:
emission |
Fluorescence emission wavelengths corresponding to the rows of the matrix, nm. |
excitation |
Fluorescence excitation wavelengths corresponding to the columns of the matrix, nm. |
dimnames |
Dimension names, copies of information above. Used only for presentation purposes. |
scale |
Scale factor, preserved through the analysis, which may be used
later to undo the scaling. Initially |
FEEM methods: plot.feem
, as.data.frame.feem
,
[.feem
, feemgrid
, feemife
,
feemscale
, feemscatter
.
feem(matrix(1:40, ncol = 8), 1:5, 1:8)
feem(
data.frame(x = 1:10, y = 21:30, z = 31:40),
emission = 'x', excitation = 'y', intensity = 'z'
)
feem(
system.file('extdata/ho_aq.csv', package = 'albatross'),
'table', sep = ','
)
feem(
system.file('extdata/F900.txt', package = 'albatross'), 'F900txt'
)
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