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Bootstrap and permutation over PLS-VIP

Source: R/nmr_data_analysis.R
bp_VIP_analysis.Rd

Bootstrap and permutation over PLS-VIP on AlpsNMR can be performed on both nmr_dataset_1D full spectra as well as nmr_dataset_peak_table peak tables.

Usage

bp_VIP_analysis(dataset, train_index, y_column, ncomp, nbootstrap = 300)

Arguments

dataset

An nmr_dataset_family object

train_index

set of index used to generate the bootstrap datasets

y_column

A string with the name of the y column (present in the metadata of the dataset)

ncomp

number of components used in the plsda models

nbootstrap

number of bootstrap dataset

Value

A list with the following elements:

  • important_vips: A list with the important vips selected

  • relevant_vips: List of vips with some relevance

  • pls_vip: Pls-VIPs of every bootstrap

  • pls_vip_perm: Pls-VIPs of every bootstrap with permuted variables

  • pls_vip_means: Pls-VIPs normaliced differences means

  • pls_vip_score_diff: Differences of pls_vip and pls_vip_perm

  • pls_models: pls models of the diferent bootstraps

  • pls_perm_models: pls permuted models of the diferent bootstraps

  • classif_rate: classification rate of the bootstrap models

  • general_model: pls model trained with all train data

  • general_CR: classification rate of the general_model

  • vips_model: pls model trained with vips selection over all train data

  • vips_CR: classification rate of the vips_model

  • error: error spected in a t distribution

  • lower_bound: lower bound of the confidence interval

  • upper_bound: upper bound of the confidence interval

Details

Use of the bootstrap and permutation methods for a more robust variable importance in the projection metric for partial least squares regression

Examples

# Data analysis for a table of integrated peaks

## Generate an artificial nmr_dataset_peak_table:
### Generate artificial metadata:
num_samples <- 32 # use an even number in this example
num_peaks <- 20
metadata <- data.frame(
    NMRExperiment = as.character(1:num_samples),
    Condition = rep(c("A", "B"), times = num_samples / 2)
)

### The matrix with peaks
peak_means <- runif(n = num_peaks, min = 300, max = 600)
peak_sd <- runif(n = num_peaks, min = 30, max = 60)
peak_matrix <- mapply(function(mu, sd) rnorm(num_samples, mu, sd),
    mu = peak_means, sd = peak_sd
)
colnames(peak_matrix) <- paste0("Peak", 1:num_peaks)

## Artificial differences depending on the condition:
peak_matrix[metadata$Condition == "A", "Peak2"] <-
    peak_matrix[metadata$Condition == "A", "Peak2"] + 70

peak_matrix[metadata$Condition == "A", "Peak6"] <-
    peak_matrix[metadata$Condition == "A", "Peak6"] - 60

### The nmr_dataset_peak_table
peak_table <- new_nmr_dataset_peak_table(
    peak_table = peak_matrix,
    metadata = list(external = metadata)
)

## We will use a double cross validation, splitting the samples with random
## subsampling both in the external and internal validation.
## The classification model will be a PLSDA, exploring at maximum 3 latent
## variables.
## The best model will be selected based on the area under the ROC curve
methodology <- plsda_auroc_vip_method(ncomp = 3)
model <- nmr_data_analysis(
    peak_table,
    y_column = "Condition",
    identity_column = NULL,
    external_val = list(iterations = 1, test_size = 0.25),
    internal_val = list(iterations = 3, test_size = 0.25),
    data_analysis_method = methodology
)
## Area under ROC for each outer cross-validation iteration:
model$outer_cv_results_digested$auroc
#> # A tibble: 1 × 3
#>   cv_outer_iteration ncomp   auc
#>                <int> <int> <dbl>
#> 1                  1     1     1

## The number of components for the bootstrap models is selected
ncomps <- model$outer_cv_results$`1`$model$ncomp
train_index <- model$train_test_partitions$outer$`1`$outer_train

# Bootstrap and permutation for VIP selection
bp_VIPS <- bp_VIP_analysis(peak_table, # Data to be analyzed
    train_index,
    y_column = "Condition",
    ncomp = ncomps,
    nbootstrap = 10
)
#> Warning: No VIPs are ranked as important
#> ℹ Try increasing the number of bootstrap iterations
#> Warning: bp_VIP_analysis: no relevant_vips found
#> ℹ You may try increasing the number of bootstraps