NEWS

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structToolbox 1.15.2

• fix ANOVA type 1
• add control_group param to ttest

structToolbox 1.13.5

• improve consistency between methods in fold change computations
• better handling of NA in fold change computations

structToolbox 1.13.4

• fix PLSDA predicted group assignment
• add option to PLSDA to use probability for yhat for predictions
• update tests

structToolbox 1.13.3

• d-ratio equations changed to match Broadhurst et al (2018)
• add tests for d-ratio
• fix PCA eigenvalues calculation

structToolbox 1.13.2

• d-ratio filter now correctly removes features
• update descriptions/documentation for missing value filters
• add tests for d-ratio

structToolbox 1.13.1

• hotfix vector_norm now correctly normalises samples to length 1
• re-sync with Bioc devel
• fix broken documentation

structToolbox 1.7.2

• internal updates to PLS
• some PLS charts have been renamed for consistency with other methods

structToolbox 1.6.1

• hotfix vector_norm now correctly normalises samples to length 1
• added vector_norm_tests

structToolbox 1.5.7

• improve NA handling in fold_change computations

structToolbox 1.5.5

• change t-test outputs to data.frame
• fix NA bug in feature_boxplot chart
• use new ontology system in place of stato

structToolbox 1.5.2

• add outputs to auto-generated documentation
• fix fold change threshold using median (#56)
• add fold change using means (#57)
• HSD param "unbalanced" is no longer ignored

structToolbox 1.5.1

• fixed broken paired tests

structToolbox 1.4.2

• fix fold change threshold using median (#56)
• HSD param "unbalanced" is no longer ignored

structToolbox 1.4.1

• fixed broken paired tests

structToolbox 1.4.0

• added VIP summary chart
• add ellipse plotting options to pca_scores_plot
• mv_sample_filter can be used in train/predict mode
• Documentation updates
• Minor issue fixes
• Add median method for fold change
• Update PQN with new inputs/outputs due to changes in pmp package
• Update SBC with new inputs/outputs due to changes in pmp package
• Update MTBLS79 due to changes in SBC

structToolbox 1.1.2

• Documentation updates
• Bug fixes

structToolbox 1.0.1

• Fix HCA bug

structToolbox 1.0.0

• Bioconductor 3.11 release

structToolbox 0.99.10

• add Metabolmics BiocView
• fix missing sections at end of vignette

structToolbox 0.99.9

• add proteomics vignette
• add mean_of_medians
• merge all vignettes
• fix bug in kfold_xval_grid

structToolbox 0.99.8

• added stratified splitting (stratified_split)
• added Gastric Cancer vignette
• add AUC metric
• add predicted and ROC plots for PLSDA

structToolbox 0.99.7

• minor documentation updates

structToolbox 0.99.6

• fix issues using class() due to changes in R 4.0.0

structToolbox 0.99.5

• fix dimnames mismatch for knn-impute
• add additional vignettes

structToolbox 0.99.4

• Add SVM, nroot transform, constant sum norm
• Add funtionality to autoscaling
• Fix some issues with permutation testing of model sequences
• Add option to impute by samples to knn
• Add custom feature labels option to pca loadings

structToolbox 0.99.3

• Fix dimnames mismatch errors
• Updated struct depency to 0.99.5

structToolbox 0.99.2

• renamed some charts containing .'s to use underscores
• renamed sbcms dataset to MTBLS79

structToolbox 0.99.1

• minor updates to pass Bioconductor checks

structToolbox 0.99.0

• use new struct v0.99.4 class constructor functions

structToolbox 0.8.4

• Final working version befor bioconductor updates

structToolbox 0.4.0 (2019-07-25)

• Minor bug fixes
• Added tsne method
• Added sbcms dataset
• Added methods related to signal/batch correction