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Convert between an eem object and a data.frame

Source: R/eem-transform.R
eem_transform.Rd

Sometimes it is easier to subset an EEM matrix if it is in a long format. This function will take an EEM matrix and turn it into a data.frame or, if it is a data.frame, convert it to an eem object.

Usage

eem_transform(eem, file = NULL, sample = NULL, location = NULL)

Arguments

eem

An object of class eem or a data.frame with three columns: ex, em, and fluor.

file

Optional. File path to the EEM data including the data file name; only used if eem is a data.frame.

sample

Optional. The name of the EEM sample; only used if eem is a data.frame.

location

Optional. The path to the directory where the file is located; only used if eem is a data.frame.

Value

Converts between an object of class eem and a data.frame with three columns:

  • ex: the excitation wavelengths

  • em: the emission wavelengths

  • fluor: the fluorescence values

Details

If you're loading samples that have been partially processed, it's recommended to set the correct processing attributes to TRUE to indicate these steps have already been performed. Use attributes(eem) to see attributes, and attr(eem, "attribute_name") <- TRUE to set them.

Examples

# Convert an EEM to a long data.frame
flat_eem <- eem_transform(example_eems[[1]])

# Convert back to an EEM object
eem_obj <- eem_transform(flat_eem)