Java version compatibility update

Bug fix

Should work with java 1.8, 11,12, 13 and 14.

Tested in BioConductor 3.12.

netDx: Version used in F1000Research software paper (BioC 3.13 devel branch)

Release as used in the software paper, ** but for BioC devel branch (3.13 pre-release) **

Pai S et al. (2021). netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks [version 2; peer review: 2 approved]
https://f1000research.com/articles/9-1239

netDx: Version used in F1000Research software paper (BioC 3.12)

Release 1.2.1, as used in the software paper
Pai S et al. (2021). netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks [version 2; peer review: 2 approved]
https://f1000research.com/articles/9-1239

Tested in BioConductor release 3.12.

Freeze of code for netDx software manuscript

Freeze of netDx 1.1.4, which accompanies the manuscript describing the software and use cases.

Stable nested CV, univariate filtering, faster sparsification

New version pre-release

• Improved sparsification > improved scalability. More control over sparsification
• runPredictor_nestedCV() now has flag for univariate filtering of features.
• Better control of ProfileToNetworkDriver through user-defined parameters passed to it.
• All code for examples run in the netDx methods paper and PSN review article (Pai S and GD Bader (2018) J Mol Biol) now moved out of this repo, leaving the code purely related to the netDx software package and tutorial examples.

** A release will follow once the code has been tested on a continuous-valued predictor and CNV-based predictor.

Details

• DESCRIPTION: Version changed to 1.0.23
• New feature: corrFeatWithOutcome.R: Correlates PC projections of features with phenotypes, allowing correlation of individual features with outcome. Tool to prioritize selected features based on which also correlate with outcome.
• New feature: sparsify3: Faster sparsifier for large datasets.
• GM_createDB.R: New parameters P2N_threshType and P2N_maxMissing: allow user control of GeneMANIA's ProfileToNetwork
• getFeatureScores.R: Option to return the full matrix of pathway scores for all splits, including those with NA. Useful when features are not consistently used across splits (e.g. univariate filtering for pathways)
• makePSN_NamedMatrix.R:
  • previous sparsify method deprecated. useSparsify2 switch now decides whether to use sparsify2 (loop-based) or sparsify3 (matrix-based, faster).
  • sparsify_edgeMax, sparsify_maxInt: parameters to control input network sparsification
  • enforces writeProfiles=TRUE when similarity metric is pearson or MI
  • similarity metric can now be "MI", without supplying custom function
  • simMetric=pearson now requires minimum 5 measures per feature.
• nWay_netSum.R: Bug fix that was causing crash. Change does not afect logic.
• runPredictor_nestedCV:
  • Added option to start with rngNum that is not 1, useful for predictors that aborted after a certain number of splits.
    • Added preFilter flag, which performs univariate lasso filtering when set.
• New sparsification methods:

• sparsify2 (to be deprecated once tests on sparsify3 are complete)
• sparsify3 (faster, matrix-based version of sparsify2)

• writeEMapInput: No longer assigns colnames to netInfo.

Automated nested CV & result plotting (beta)

Major upgrade to netDx functionality but in beta stage. Wait for the next release to get a stable version.

• New functions to plot predictor results, including performance views (ROC/PR curves), Cyrest-based generation of EnrichmentMaps of selected features, and integrated PSN view.
  • Includes plotAllResults() which will do all this in a single function call.
• New R function to run nested cross-validation in single function call. Takes generic function for custom feature design as input.
• Three R notebooks illustrating predictor plotting and automated nested cross-validation. See .Rmd files in examples/ directory.

stable release

First release.
Examples for medulloblastoma 4-way classification and breast cancer luminal A binary classification run and work. Tested on 170831.
Functions to plot results not included as yet.