Read excitation-emission fluorescence matrix (eem)
eem_read(file, recursive = FALSE, import_function)
| 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 |
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.
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)].
file <- system.file("extdata/cary/scans_day_1/", package = "eemR") eems <- eem_read(file, recursive = TRUE, import_function = "cary")