# Data processing & analysis tools for Metabolomics and other omics

## Documentation for package ‘structToolbox’ version 1.2.0

- 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 | Analysis of Variance
as_data_frame | Convert to data.frame
as_data_frame-method | Convert to data.frame
AUC | Area under ROC curve
autoscale | Autoscaling

## -- B --

balanced_accuracy | Balanced Accuracy
blank_filter | Blank filter
blank_filter_hist | Histogram of blank filter fold changes
bootstrap | Bootstrap resampling

## -- C --

calculate | Calculate metric
calculate-method | Calculate metric
chart_plot | chart_plot method
chart_plot-method | chart_plot method
classical_lsq | Univariate Classical Least Squares Regression
compare_dist | Compare distributions
confounders_clsq | Check for confounding factors
confounders_lsq_barchart | Confounding factor relative change barchart
confounders_lsq_boxplot | Confounding factor relative change boxplot
constant_sum_norm | Normalisation to constant sum
corr_coef | Correlation coefficient

## -- D --

DatasetExperiment_boxplot | Feature distribution histogram
DatasetExperiment_dist | Feature distribution histogram
DatasetExperiment_factor_boxplot | Factor boxplot
DatasetExperiment_heatmap | DatasetExperiment heatmap
DFA | Discriminant Factor Analysis
dfa_scores_plot | DFA scores plot
dratio_filter | Dispersion ratio filter

## -- F --

feature_boxplot | Feature boxplot
feature_profile | Feature profile
filter_by_name | Filter by name
filter_na_count | Minimum number of measured values filter
filter_smeta | Filter by sample meta data
fisher_exact | Fisher Exact Test
fold_change | Fold change
fold_change_int | Fold change for interactions between factors
fold_change_plot | Fold change plot
forward_selection_by_rank | Forward selection by rank
fs_line | Forward selection line plot

## -- G --

glog_opt_plot | Glog optimisation
glog_transform | Generalised logarithmic transform
grid_search_1d | One dimensional grid search
gs_line | Grid search line plot

## -- H --

HCA | Hierarchical Cluster Analysis
hca_dendrogram | HCA dendrogram
HSD | Tukey's Honest Significant Difference
HSDEM | Tukey's Honest Significant Difference using estimated marginal means

## -- K --

kfoldxcv_grid | k-fold cross validation plot
kfoldxcv_metric | kfoldxcv metric plot
kfold_xval | k-fold cross-validation
knn_impute | kNN missing value imputation
kw_p_hist | Histogram of p values
kw_rank_sum | Kruskal-Wallis rank sum test

## -- L --

linear_model | Linear model
log_transform | logarithm transform

## -- M --

mean_centre | Mean centre
mean_of_medians | Mean of medians
mixed_effect | Mixed effects model
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 | Missing value boxplots
mv_feature_filter | Filter by fraction missing values
mv_feature_filter_hist | Histogram of missing values per feature
mv_histogram | Missing value histogram
mv_sample_filter | Missing value sample filter
mv_sample_filter_hist | Histogram of missing values per sample

## -- N --

nroot_transform | nth root transform

## -- P --

pairs_filter | Pairs filter
pareto_scale | Pareto scaling
PCA | Principal Component Analysis (PCA)
pca_biplot | PCA biplot
pca_correlation_plot | PCA correlation plot
pca_dstat_plot | d-statistic plot
pca_loadings_plot | PCA loadings plot
pca_scores_plot | PCA scores plot
pca_scree_plot | Scree plot
permutation_test | Permutation test
permutation_test_plot | permutation_test_plot class
permute_sample_order | Permute Sample Order
PLSDA | Partial least squares discriminant analysis
plsda_predicted_plot | PLSDA predicted plot
plsda_regcoeff_plot | plsda_regcoeff_plot class
plsda_roc_plot | PLSDA ROC plot
plsda_scores_plot | PLSDA scores plot
plsda_vip_plot | PLSDA VIP plot
PLSR | Partial least squares regression
plsr_cook_dist | Cook's distance barchart
plsr_prediction_plot | PLSR prediction plot
plsr_qq_plot | PLSR QQ plot
plsr_residual_hist | PLSR residuals histogram
pqn_norm | Probabilistic Quotient Normalisation (PQN)
pqn_norm_hist | PQN coefficient histogram
prop_na | Fisher's exact test for missing values

## -- R --

rsd_filter | RSD filter
rsd_filter_hist | RSD histogram
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 (R-squared)

## -- S --

sb_corr | Signal/batch correction for mass spectrometry data
split_data | Split data
stratified_split | Stratified sampling
structToolbox | structToolbox: Examples of tools built using the Statistics in R Using Class Templates (struct) package
SVM | Support Vector Machine Classifier
svm_plot_2d | SVM scatter plot

## -- T --

tSNE | tSNE
tSNE_scatter | Feature boxplot
ttest | t-test

## -- V --

vec_norm | Vector normalisation

## -- W --

wilcox_p_hist | Histogram of p values
wilcox_test | wilcoxon signed rank test