ppm_VIP_vector: Feature selection and validation in multivariate analysis

In AlpsNMR: Automated spectraL Processing System for NMR

Description

Numeric VIPs vector

Usage

ppm_VIP_vector(VIPs)

Arguments

VIPs	a dataframe from the model_VIP(MVObj) function. It requires a "ppms" variable

Details

The function extracts the VIPs vector (numeric) from the model_VIP(MVObj) function. It is not necessary if you have the ppm values in a numeric vector. This is needed in case that an automated pipeline is applied, connecting the output from model_VIP(MVObj) to nmr_identify_regions family functions.

Value

a numeric ppm vector ready to be identified with nmr_identify_regions_blood, nmr_identify_cell or nmr_identify_regions_urine

Examples

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

## Example of MUVR usage
# 1.Build a model with the X data from your nmr object and your class:
#MVObj <- rdCV_PLS_RF(nmr_data(nmr_peak_table),
#Y = nmr_peak_table_completed$Timepoint)

# 2.Model performance
#confusion_matrix(MVObj)

# 3.Plotting the model
#MUVR_model_plot(MVObj)

# 4.Permutation test
#permutations <- permutation_test_model(MVObj, nPerm = 50)

# 5.Plotting permutation test results
#permutation_test_plot(MVObj, permutations, model = "Mid", type = "t")

# 6.p-Value
#p.value <- p_value_perm(MVObj$miss[["mid"]], permutations[, "Mid"])

# 7.Significant variables
#VIPs <- model_VIP(MVObj)

# 8.Identification
#results <- nmr_identify_regions_blood(ppm_VIP_vector(VIPs))

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