permutation_test_model: Permutation test

In AlpsNMR: Automated spectraL Processing System for NMR

Description

Make permutations with data and default settings from an nmr_data_analysis_method

Usage

permutation_test_model(
  dataset,
  y_column,
  identity_column,
  external_val,
  internal_val,
  data_analysis_method,
  nPerm = 50
)

Arguments

dataset	An nmr_dataset_family object
y_column	A string with the name of the y column (present in the metadata of the dataset)
identity_column	NULL or a string with the name of the identity column (present in the metadata of the dataset).
external_val	A list with two elements: iterations and test_size. See random_subsampling for further details
internal_val	A list with two elements: iterations and test_size. See random_subsampling for further details
data_analysis_method	An nmr_data_analysis_method object
nPerm	number of permutations

Value

A permutation matrix with permuted values

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),
    stringsAsFactors = FALSE
)

### 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)
)

methodology <- plsda_auroc_vip_method(ncomp = 3)
model <- nmr_data_analysis(
    peak_table,
    y_column = "Condition",
    identity_column = NULL,
    external_val = list(iterations = 3, test_size = 0.25),
    internal_val = list(iterations = 3, test_size = 0.25),
    data_analysis_method = methodology
)

p = permutation_test_model(peak_table,
                           y_column = "Condition",
                           identity_column = NULL,
                           external_val = list(iterations = 3, test_size = 0.25),
                           internal_val = list(iterations = 3, test_size = 0.25),
                           data_analysis_method = methodology, 
                           nPerm = 10)
                           

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