Read excitation-emission fluorescence matrix (eem)
Arguments
- file
File name or folder containing fluorescence file(s).
- recursive
logical. Should the listing recurse into directories?
- import_function
Either a character or a user-defined function to import a single eem. If a character, it should be one of "cary", "aqualog", "shimadzu", "fluoromax4". See
browseVignettes("eemR")to learn how to create your own import function.
Value
If file is a single filename:
An object of class eem containing:
sample The file name of the eem.
x A matrix with fluorescence values.
em Emission vector of wavelengths.
ex Excitation vector of wavelengths.
If file is a folder, the function returns an object of class
eemlist which is simply a list of eem.
Details
At the moment, Cary Eclipse, Aqualog and Shimadzu EEMs are supported.
eemR will automatically try to determine from which
spectrofluorometer the files originate and load the data accordingly. Note
that EEMs are reshaped so X[1, 1] represents the fluorescence intensity at
X[min(ex), min(em)].
Examples
file <- system.file("extdata/cary/scans_day_1/", package = "eemR")
eems <- eem_read(file, recursive = TRUE, import_function = "cary")