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Import Oxygen Flux Data From One Or More Oroboros-O2K formatted .csv files.

Source: R/read_o2k_oxy_csv.R
read_o2k_oxy_csv.Rd

A wrapper for three other tidymito functions (o2k_oxy_to_list(), o2k_oxy_list_to_tbl(), and oxy_tbl_format()) with added code links allowing a user to go from the .csv file exported from the Oroboros-O2K to a fully processed tibble. This can be applied to a single csv file or multiple files within a single directory, but in all cases will result in a single output tibble.

.csv files matching a supplied regex pattern will be identified, 'events' (user defined durin the run, e.g: addition of Proline) will be identified and windows will be automatically selected based on the stability of the oxygen flux readings (completed separately for each state in each chamber). Average values per window will then be formatted and returned.

If specified, sample information can be extracted from the .csv file names and added into the output.

Usage

read_o2k_oxy_csv(
  file_id = "*.csv",
  directory_path = "NULL",
  exclude_events = "none",
  treat_opening = "after",
  window_sizes = 15,
  change_thresholds = 1,
  format_output = TRUE,
  sample_identifiers = "NULL",
  info_col = "filename",
  wide_output = FALSE
)

Arguments

file_id

A regex string that identifies the input csv files to process. Suggested to end in ".csv", by default set to "*.csv" (matching all .csv files in the specified directory). For more information on regex patterns I recommend the stringr cheatsheets.

directory_path

A path to the directory containing the relevant csv files. Defaults to the current working directory.

exclude_events

A character vector with any events (e.g: addition of substrates or uncouplers) that you wish to ignore. See o2k_oxy_list_to_tbl() for more details. If multiple events occur simultaneously (e.g 11As and 11Tm), all but one should be excluded.

treat_opening

In instances where a chamber is opened during a run, should the window be place before or after this event? Passes argument to o2k_oxy_list_to_tbl().

window_sizes

A numeric vector (or vectors) specifying the window size. Defined in terms of instrument recordings (i.e: if the Oroboros returns a reading every 2 seconds, a specified window size of '10' equates to a window in absolute terms of 20seconds.)

change_thresholds

A numeric value specifying the tolerance for change between consecutive O2K measurements. Changes less than this value will be considered 'stable'.

format_output

A TRUE/FALSE statement about whether to neaten and format the output.

sample_identifiers

A vector of character strings that can be used to identify a sample.

info_col

A character string of the name of the column containing the information to extract. Defaults to filename.

wide_output

Whether to return a wide (one column per state, one row per sample) or longer (each row is one state in one sample) tibble. Must be TRUE or FALSE.

Value

A tibble (either wide, long, or unformatted)

See also

Other read o2k files: o2k_oxy_list_to_tbl(), o2k_oxy_to_list(), read_o2k_oxy_xlsx()

Examples

 # basic functionality: read in data without specifying any formatting steps or window sizes:
 testdata <- read_o2k_oxy_csv(
   file_id = "2025-03-03.*.csv", # using provided example script
   directory_path = "path/to/data/",
   exclude_events = c("11As")
   )
#> Warning: No sample identifers supplied, returning unformatted tibble

 # basic functionality: read in data without specifying any formatting steps or window sizes:
 testdata <- read_o2k_oxy_csv(
   file_id = "2025-03-03.*.csv", # using provided example script
   directory_path = "path/to/data/",
   exclude_events = c("11As"),  # as this is added at the same time as 11Tm, remove 11As
   treat_opening = "after",  # if a chamber is opened during a state, place the window after then chamber has re-oxygenated and closed.
   window_sizes = 15,  # if a measurement is taken every 2 seconds, the signal must be stable for 30 (2x15) seconds to pass the cutoff.
   change_thresholds = 1,
   format_output = TRUE, # select that you want the output tibble to be formatted
   sample_identifiers = c("NDi1-OE x gal4", "NDi1-OE ctrl"), # specify your unique sample identifiers
   wide_output = FALSE # specify that you want the data to be returned in a 'wide' format.
   )
#> Sample identifiers used. Ensure that all filenames have identifiers for both Chambers.