Data processing & analysis tools for Metabolomics and other omics

Documentation for package ‘structToolbox’ version 1.0.1

Help Pages

-- A --

-- B --

-- 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

-- 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 --

-- V --

Vector normalisation

-- W --

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