rdCV_PLS_RF_ML: Deprecated function Feature selection and validation in...

In AlpsNMR: Automated spectraL Processing System for NMR

Description

Statistical analysis and feature selection in a repeated double cross-validation frame based on the partial least squares (PLS) or random forest (RF) analyses using an algorithm for multivariate modelling with minimally biased variable selection (MUVR) from the MUVR package. The function rdCV_PLS_RF_ML allows the multilevel comparison, especially useful in crossover or longitudinal studies (2 timepoints) considering the same individual (it requires 2 samples of the same observation).

Usage

rdCV_PLS_RF_ML(
  nmr_peak_table,
  label,
  scale = TRUE,
  nRep = 10,
  nOuter = 5,
  nInner,
  varRatio = 0.75,
  DA = FALSE,
  fitness = "MISS",
  method = "PLS",
  ML = TRUE,
  modReturn = FALSE,
  logg = FALSE,
  parallel = TRUE
)

Arguments

nmr_peak_table	an AlpsNMR integration object (2 classes)
label	the name of the variable to test (e.g. "Timepoint")

Value

a MUVR model containing selection parameters, validation and fitness

References

Shi,L. et al. (2018) Variable selection and validation in multivariate modelling. Bioinformatics.

See Also

Other nmr_dataset_1D functions: [.nmr_dataset_1D(), computes_peak_width_ppm(), file_lister(), files_to_rDolphin(), format.nmr_dataset_1D(), is.nmr_dataset_1D(), load_and_save_functions, new_nmr_dataset_1D(), nmr_align_find_ref(), nmr_baseline_removal(), nmr_baseline_threshold(), nmr_exclude_region(), nmr_integrate_regions(), nmr_interpolate_1D(), nmr_meta_add(), nmr_meta_export(), nmr_meta_get_column(), nmr_meta_get(), nmr_normalize(), nmr_pca_build_model(), nmr_pca_outliers_filter(), nmr_pca_outliers_plot(), nmr_pca_outliers_robust(), nmr_pca_outliers(), nmr_ppm_resolution(), plot.nmr_dataset_1D(), plot_webgl(), print.nmr_dataset_1D(), rdCV_PLS_RF(), save_files_to_rDolphin(), to_ChemoSpec(), validate_nmr_dataset_peak_table(), validate_nmr_dataset()

Examples

message("MUVR is not compatible with Bioconductor, 
use bp_kfold_VIP_analysis method instead")

AlpsNMR documentation built on April 1, 2021, 6:02 p.m.