Correct Retention Time (RT) in a Spectral Database — correct_database

This function corrects the retention time (RT) information in a spectral database using a reference table of internal standards from an experiment and a corresponding table from the database. The correction can be performed using different methods such as polynomial fitting or loess smoothing.

correct_database_rt(
  experiment.is.table,
  database.is.table,
  database,
  method = c("polyline", "loess"),
  poly = c(1, 2, 3, 4, 5),
  degree = c(1, 2),
  path = "."
)

Arguments

experiment.is.table: A data frame containing the internal standards (IS) information from the experiment. It should include columns for retention time (RT) and other relevant information.
database.is.table: A data frame containing the internal standards (IS) information from the database. It should include retention time (RT) values corresponding to the database spectra.
database: A `databaseClass` object that contains the database to be corrected.
method: A character string specifying the method for RT correction. Options are `"polyline"` for polynomial fitting or `"loess"` for loess smoothing. Defaults to `"polyline"`.
poly: A numeric vector specifying the polynomial degrees to use for the correction when `method = "polyline"`. Defaults to `c(1, 2, 3, 4, 5)`.
degree: A numeric vector specifying the degree for loess smoothing when `method = "loess"`. Defaults to `c(1, 2)`.
path: A character string specifying the directory to save intermediate files. Defaults to the current directory (`"."`).

Value

A `databaseClass` object with corrected RT values.

Details

The function first writes a table of features from the database to a CSV file, which is used in the `correct_rt` function to perform the retention time correction based on the provided internal standards tables. The corrected RT values are then updated in the `databaseClass` object.

The `method` parameter allows the user to choose between polynomial fitting (`"polyline"`) and loess smoothing (`"loess"`) for the RT correction. The `poly` and `degree` parameters specify the details of the polynomial or loess fitting, respectively.

Intermediate files generated during the process are saved in the directory specified by `path`, but are removed after use.

Author

Xiaotao Shen xiaotao.shen@outlook.com

Examples

if (FALSE) { # \dontrun{
# Correct RT in a database using polynomial fitting
corrected_db <- correct_database_rt(
  experiment.is.table = experiment_table,
  database.is.table = database_table,
  database = db_object,
  method = "polyline",
  poly = 1:3,
  degree = 2,
  path = "output_directory"
)
} # }