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Load, clean, and process EEMs and absorbance data

Source: R/run-eems.R
run_eems.Rd

The main high-level function of the eemanalyzeR package. It is designed for users who want a fast, automated workflow without needing to write complex R code or string together a bunch of processing functions. By pointing the function to a folder of raw EEMs and absorbance data, the function performs the full processing pipeline from start to finish.

Usage

run_eems(
  input_dir,
  output_dir = NA,
  filename = NA,
  interactive = TRUE,
  blanklist = NULL,
  qaqc_checks = TRUE,
  ...
)

Arguments

input_dir

Path to folder containing raw EEMs and/or absorbance files.

output_dir

Path to save the processed data.

filename

A character string, used for file names.

interactive

Logical, used to determine if user input should be used.

blanklist

eemlist of blank files to subtract from samples. Automatically uses instrument blanks if not provided.

qaqc_checks

Logical, should user QA/QC files be used to check data?

...

additional arguments used to make one time modifications to processing arguments and plotting (plot.eemlist). List of optional arguments to modify within the processing are located in default_config. See details for more info on modifying processing configuration.

Value

The following files are saved to the output directory specified. The list contains:

  • eemlist: the eemlist

  • abslist: the abslist

  • readme: a character vector containing information about the data processing steps

  • meta: the metadata associated with the samples, may be NULL if not provided

  • indices: a list of EEMs and absorbance indices, may be NULL if not provided

  • eem_plot: a list of EEMs plots, may be NULL if not provided

  • abs_plot: a ggplot2 object of the absorbance data, may be NULL if not provided

Details

The only requirement to use this wrapper function to process EEMs and absorbance data is an input directory containing the raw data files and a metadata spreadsheet. However, there are many optional arguments for the user to modify the EEMs and absorbance processing. The names and default values for these arguments can be found in the documentation for the default_config.

There are four ways for user to use and modify the processing configuration defaults.

  • Option 1: User doesn't change anything, the package defaults are used by run_eems.

  • Option 2: User creates a file (stored on their computer) that has processing defaults that eemanalyzeR pulls from at load time. This is created using the edit_user_config() function.

  • Option 3: User modifies the defaults BEFORE using the run_eems function using modify_config() function. This modifies the settings for the R session and will be applied to any data processing that occurs until the package is reloaded or the R session is restarted. After the package is reloaded the defaults revert back to the package defaults or (if they exist) user defaults.

  • Option 4: User supplies arguments to run_eems function that modify processing ONLY during that run. These configuration options will not persist across multiple tries of run_eems and must be specified each time, but the argument values will be reported in the readme file.

Note

Currently run_eems does not allow for custom import or index functions.