feem: Create a fluorescence excitation-emission matrix object
In albatross: PARAFAC Analysis of Fluorescence Excitation-Emission Matrices

View source: R/feem.R

feem	R Documentation

Create a fluorescence excitation-emission matrix object

Description

Functions to create fluorescence excitation-emission matrix objects from R matrices coupled with excitation and emission wavelengths, three-column data.frames containing 3{ (\lambda_\mathrm{em}, \lambda_\mathrm{ex}, I)

Usage

  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, ...)

Arguments

`x`	The source of the information to create a FEEM object from: a matrix, a three-column `data.frame`, a file path as a single string, or a connection. If converting a matrix, its rows should correspond to different fluorescence emission wavelengths specified in the `emission` argument; conversely, its columns should correspond to excitation wavelengths specified in the `excitation` argument. If converting a `data.frame`, it should have exactly three columns containing emission wavelengths, excitation wavelength, and intensity values. The names of the columns are expected to be “emission”, “excitation”, and “intensity”, respectively, but can be overridden using namesake arguments. If reading a single file by file path or connection, the `format` argument must specify the kind of file to parse, see below.
`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 `data.frame`, this optional argument specifies the name of the column containing the emission wavelengths.
`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 `data.frame`, this optional argument specifies the name of the column containing the excitation wavelengths.
`intensity`	If converting a `data.frame`, this optional argument specifies the name of the column containing the fluorescence intensities.
`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`	table The FEEM is assumed to be stored as a plain text matrix, readable using `read.table`, with the first column and the first row containing wavelengths. For example, it is possible to import CSV files obtained from a HORIBA Aqualog® fluorometer by using `feem(file, 'table', sep = ',')`. Rows are assumed to correspond to emission wavelengths, columns are assumed to correspond to excitation wavelengths; if that's not the case, set the `transpose` argument to `TRUE`. If there are unmeasured points in the spectrum (e.g. the anti-Stokes area) encoded as special numbers (e.g. stored as zeroes or `-100`), specify their values as the `na` argument (numeric vector). The function will check for triangles filled with these values (such that a threshold 3{\Delta 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}

Details

Transposing a feem object using t will remove the class attribute, returning an ordinary matrix.

Value

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 `1`.

Examples

  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'
  )

albatross documentation built on May 29, 2024, 9:10 a.m.