# Data processing & analysis tools for Metabolomics and other omics

## Documentation for package ‘structToolbox’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G H K L M N P R S T V W

## -- A --

ANOVA | ANOVA
as_data_frame | Convert to data.frame
as_data_frame-method | Convert to data.frame
AUC | Area under ROC
autoscale | Autoscale

## -- B --

balanced_accuracy | Balanced Accuracy
blank_filter | Blank filter
blank_filter_hist | plot for blank filter
bootstrap | Bootstrap class

## -- C --

calculate | Calculate metric
calculate-method | Calculate metric
chart_plot | chart_plot method
chart_plot-method | chart_plot method
classical_lsq | Classical Least Squares regression
compare_dist | Compare distributions
confounders_clsq | Check for confounding factors in ttest
confounders_lsq_barchart | barchart of percent change
confounders_lsq_boxplot | boxplot of percent change
constant_sum_norm | Normalisation to constant sum
corr_coef | Correlation Coefficient

## -- D --

DatasetExperiment_boxplot | DatasetExperiment boxplot
DatasetExperiment_dist | Distribution plot
DatasetExperiment_factor_barchart | DatasetExperiment_factor_barchart class
DatasetExperiment_heatmap | DatasetExperiment_heatmap class
DFA | Discriminant Factor Analysis (DFA)
dfa_scores_plot | dfa_scores_plot class
dratio_filter | D ratio filter

## -- F --

feature_boxplot | Feature boxplots
feature_profile | Feature profile class
filter_by_name | Filter by name
filter_na_count | filter_na_count class
filter_smeta | filter_smeta class
fisher_exact | fisher_exact class
fold_change | fold change class
fold_change_int | fold change for interactions class
fold_change_plot | fold_change plot
forward_selection_byrank | forward selection by rank
fs_line | forward_selection_plot

## -- G --

glog_opt_plot | glog transform optimisation plot
glog_transform | glog transform
grid_search_1d | grid_search_1d class
gs_line | grid_search_plot

## -- H --

HCA | HCA method class
hca_dendrogram | hca_dendrogram class
HSD | HSD model class
HSDEM | HSD model class using estimated marginal means

## -- K --

kfoldxcv_grid | kfoldxcv_grid class
kfoldxcv_metric | kfoldxcv_metric class
kfold_xval | kfold_xval model class
knn_impute | knn missing value imputation
kw_p_hist | plot histogram of p values
kw_rank_sum | kruskal-wallis model class

## -- L --

linear_model | linear model class
log_transform | log transform

## -- M --

mean_centre | mean_centre model class
mean_of_medians | Mean of median adjustment
mixed_effect | Mixed Effects model class
model_apply | Apply method
model_apply-method | Apply method
model_predict | Model prediction
model_predict-method | Model prediction
model_reverse | Reverse preprocessing
model_reverse-method | Reverse preprocessing
model_train | Train a model
model_train-method | Train a model
MTBLS79_DatasetExperiment | MTBLS79: Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control
mv_boxplot | mv_boxplot class
mv_feature_filter | filter features by fraction of missing values
mv_feature_filter_hist | plot for missing value sample filter
mv_histogram | mv_histogram class
mv_sample_filter | Missing value filter (samples)
mv_sample_filter_hist | plot for missing value sample filter

## -- N --

nroot_transform | nroot transform

## -- P --

pairs_filter | Pairs filter
pareto_scale | Pareto scaling
PCA | PCA model class
pca_biplot_plot | pca_biplot_plot class
pca_correlation_plot | pca_correlation_plot class
pca_dstat_plot | pca_dstat_plot_plot class
pca_loadings_plot | pca_loadings_plot class
pca_scores_plot | pca_scores_plot class
pca_scree_plot | pca_scree_plot_plot class
permutation_test | Permutation test class
permutation_test_plot | permutation_test_plot class
permute_sample_order | permute_sample_order class
PLSDA | PLSDA model class
plsda_predicted_plot | plsda_predicted_plot class
plsda_regcoeff_plot | plsda_regcoeff_plot class
plsda_roc_plot | plsda_roc_plot class
plsda_scores_plot | plsda_scores_plot class
plsda_vip_plot | plsda_vip_plot class
PLSR | PLSR model class
plsr_cook_dist | plsr_cook_dist class
plsr_prediction_plot | plsr_prediction_plot class
plsr_qq_plot | plsr_qq_plot class
plsr_residual_hist | plsr_residual_hist class
pqn_norm | Probabilistic Quotient Normalisation
pqn_norm_hist | plot for PQN normalisation
prop_na | prop_na model class

## -- R --

rsd_filter | rsd filter
rsd_filter_hist | plot for rsd filter
run | Runs an iterator, applying the chosen model multiple times.
run-method | Runs an iterator, applying the chosen model multiple times.
r_squared | Coefficient of determination class

## -- S --

sb_corr | sbcms
split_data | Split data into subsets
stratified_split | Stratified sampling
structToolbox | structToolbox: Examples of tools built using the Statistics in R Using Class Templates (struct) package
SVM | SVM model classifier
svm_plot_2d | SVM boundary plot (2d)

## -- T --

tSNE | tSNE method class
tSNE_scatter | tSNE_scatter class
ttest | t-test model class

## -- V --

vec_norm | Vector normalisation

## -- W --

wilcox_p_hist | plot histogram of p values
wilcox_test | Wilcoxon signed rank test method class