Man pages for computational-metabolomics/structToolbox
Data processing & analysis tools for Metabolomics and other omics

ANOVAAnalysis of Variance
as_data_frameConvert to data.frame
AUCArea under ROC curve
autoscaleAutoscaling
balanced_accuracyBalanced Accuracy
blank_filterBlank filter
blank_filter_histHistogram of blank filter fold changes
bootstrapBootstrap resampling
calculateCalculate metric
chart_plotchart_plot method
classical_lsqUnivariate Classical Least Squares Regression
compare_distCompare distributions
confounders_clsqCheck for confounding factors
confounders_lsq_barchartConfounding factor relative change barchart
confounders_lsq_boxplotConfounding factor relative change boxplot
constant_sum_normNormalisation to constant sum
corr_coefCorrelation coefficient
DatasetExperiment_boxplotFeature distribution histogram
DatasetExperiment_distFeature distribution histogram
DatasetExperiment_factor_boxplotFactor boxplot
DatasetExperiment_heatmapDatasetExperiment heatmap
DFADiscriminant Factor Analysis
dfa_scores_plotDFA scores plot
dratio_filterDispersion ratio filter
feature_boxplotFeature boxplot
feature_profileFeature profile
filter_by_nameFilter by name
filter_na_countMinimum number of measured values filter
filter_smetaFilter by sample meta data
fisher_exactFisher Exact Test
fold_changeFold change
fold_change_intFold change for interactions between factors
fold_change_plotFold change plot
forward_selection_by_rankForward selection by rank
fs_lineForward selection line plot
glog_opt_plotGlog optimisation
glog_transformGeneralised logarithmic transform
grid_search_1dOne dimensional grid search
gs_lineGrid search line plot
HCAHierarchical Cluster Analysis
hca_dendrogramHCA dendrogram
HSDTukey's Honest Significant Difference
HSDEMTukey's Honest Significant Difference using estimated...
kfoldxcv_gridk-fold cross validation plot
kfoldxcv_metrickfoldxcv metric plot
kfold_xvalk-fold cross-validation
knn_imputekNN missing value imputation
kw_p_histHistogram of p values
kw_rank_sumKruskal-Wallis rank sum test
linear_modelLinear model
log_transformlogarithm transform
mean_centreMean centre
mean_of_mediansMean of medians
mixed_effectMixed effects model
model_applyApply method
model_predictModel prediction
model_reverseReverse preprocessing
model_trainTrain a model
MTBLS79_DatasetExperimentMTBLS79: Direct infusion mass spectrometry metabolomics...
mv_boxplotMissing value boxplots
mv_feature_filterFilter by fraction missing values
mv_feature_filter_histHistogram of missing values per feature
mv_histogramMissing value histogram
mv_sample_filterMissing value sample filter
mv_sample_filter_histHistogram of missing values per sample
nroot_transformnth root transform
pairs_filterPairs filter
PCAPrincipal Component Analysis (PCA)
pca_biplotPCA biplot
pca_correlation_plotPCA correlation plot
pca_dstat_plotd-statistic plot
pca_loadings_plotPCA loadings plot
pca_scores_plotPCA scores plot
pca_scree_plotScree plot
permutation_testPermutation test
permutation_test_plotpermutation_test_plot class
permute_sample_orderPermute Sample Order
PLSDAPartial least squares discriminant analysis
plsda_predicted_plotPLSDA predicted plot
plsda_regcoeff_plotplsda_regcoeff_plot class
plsda_roc_plotPLSDA ROC plot
plsda_scores_plotPLSDA scores plot
plsda_vip_plotPLSDA VIP plot
PLSRPartial least squares regression
plsr_cook_distCook's distance barchart
plsr_prediction_plotPLSR prediction plot
plsr_qq_plotPLSR QQ plot
plsr_residual_histPLSR residuals histogram
pqn_normProbabilistic Quotient Normalisation (PQN)
pqn_norm_histPQN coefficient histogram
prop_naFisher's exact test for missing values
rsd_filterRSD filter
rsd_filter_histRSD histogram
r_squaredCoefficient of determination (R-squared)
runRuns an iterator, applying the chosen model multiple times.
sb_corrSignal/batch correction for mass spectrometry data
split_dataSplit data
stratified_splitStratified sampling
structToolboxstructToolbox: Examples of tools built using the Statistics...
SVMSupport Vector Machine Classifier
svm_plot_2dSVM scatter plot
tSNEtSNE
tSNE_scatterFeature boxplot
ttestt-test
vec_normVector normalisation
wilcox_p_histHistogram of p values
wilcox_testwilcoxon signed rank test
computational-metabolomics/structToolbox documentation built on Nov. 17, 2020, 2:27 p.m.