Data processing & analysis tools for Metabolomics and other omics

Documentation for package ‘structToolbox’ version 1.17.3

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-- A --

-- 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

-- E --

Equal group sized sampling

-- F --

feature_boxplot	Feature boxplot
feature_profile	Feature profile
feature_profile_array	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 features by 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 --

nth root transform

-- O --

ontology_cache	ontology cache
OPLSDA	Orthogonal Partial Least Squares regression
OPLSR	Orthogonal Partial Least Squares regression

-- 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_feature_importance_plot	PLSDA feature importance summary plot
plsda_predicted_plot	PLSDA predicted plot
plsda_roc_plot	PLSDA ROC plot
plsda_scores_plot	PLSDA scores 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
pls_regcoeff_plot	pls_regcoeff_plot class
pls_scores_plot	PLSDA scores plot
pls_scores_plot,	PLSDA scores plot
pls_vip_plot	PLSDA VIP plot
pqn_norm	Probabilistic Quotient Normalisation (PQN)
pqn_norm_hist	PQN coefficient histogram
prop_na	Fisher's exact test for missing values

-- R --

resample	Data resampling
resample_chart	resample_chart class
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
scatter_chart	Group scatter chart
split_data	Split data
stratified_split	Stratified sampling
SVM	Support Vector Machine Classifier
svm_plot_2d	SVM scatter plot

-- T --

-- V --

Vector normalisation

-- W --

wilcox_p_hist	Histogram of p values
wilcox_test	wilcoxon signed rank test