eemR (version 1.0.2)

eem_read: Read excitation-emission fluorescence matrix (eem)

Description

Read excitation-emission fluorescence matrix (eem)

Usage

eem_read(file, recursive = FALSE, 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.

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.

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")