selective_measuring: Selective Measuring

In FastRet: Retention Time Prediction in Liquid Chromatography

Selective Measuring

Description

The function adjust_frm() is used to modify existing FastRet models based on changes in chromatographic conditions. It requires a set of molecules with measured retention times on both the original and new column. This function selects a sensible subset of molecules from the original dataset for re-measurement. The selection process includes:

1. Generating chemical descriptors from the SMILES strings of the molecules. These are the features used by train_frm() and adjust_frm().

2. Standardizing chemical descriptors to have zero mean and unit variance.

3. Training a Ridge Regression model with the standardized chemical descriptors as features and the retention times as the target variable.

4. Scaling the chemical descriptors by coefficients of the Ridge Regression model.

5. Applying PAM clustering on the entire dataset, which includes the scaled chemical descriptors and the retention times.

6. Returning the clustering results, which include the cluster assignments, the medoid indicators, and the raw data.

Usage

selective_measuring(raw_data, k_cluster = 25, verbose = 1)

Arguments

raw_data	The raw data to be processed. Must be a dataframe with columns NAME, RT and SMILES.
k_cluster	The number of clusters for PAM clustering.
verbose	The level of verbosity.

Value

A list containing the following elements:

• clustering: a data frame with raw data, cluster assignments, and medoid indicators

• clobj: the PAM clustering object

• coefs: the coefficients from the Ridge Regression model

• model: the Ridge Regression model

• df: the preprocessed data

• dfz: the standardized features

• dfzb: the features scaled by coefficients of the Ridge Regression model

Examples

x <- selective_measuring(RP[1:50, ], k = 5, verbose = 0)
# For the sake of a short runtime, only the first 50 rows of the RP dataset
# were used in this example. In practice, you should always use the entire
# dataset to find the optimal subset for re-measurement.

FastRet documentation built on June 25, 2024, 5:07 p.m.