Version 6.1.0 and latest publications

We are proud to announce our new update 6.1.0 available on CRAN. It was supposed to be a small patch but we got slightly ahead of ourselves. Special thanks to the mixOmics French’Oz developers, Dr Florian Rohart (University of Queensland, Brisbane) and Mr François Bartolo (Université de Toulouse, France), as well as several users who have been using our latest methods and reported bugs or suggested improvements on our bitbucket issue website.

Manuscripts and publication update

  • Rohart F.,  Matigian N., Eslami A., Bougeard S and Lê Cao, K. A..MINT: A multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. Now available on bioRxiv!

  • Singh A, Gautier B, Shannon C, Vacher M, Rohart F, Tebbutt S, K-A. Lê Cao. DIABLO – multi-omics data integration for biomarker discovery. Manuscript available in bioRxiv.

  • K-A. Lê Cao*, ME Costello*,  VA Lakis, F Bartolo, XY Chua, R Brazeilles, P Rondeau. (2016) MixMC: Multivariate insights into Microbial Communities.PLoS ONE 11(8): e0160169 [link]

List of changes in mixOmics 6.1.0 (in NEWS file)

In short,
– cimDIABLO argument ‘corThreshold’ replaced by ‘cutoff’
– new plots of tune and perf results now available
– tune function for block.splsda/DIABLO method
– auroc for supervised methods

New features:

1- auroc function applicable for (mint).(block).(s)plsda objects. AUc values also included in perf and tune functions (except mixDIABLO module)
2- tune.block.splsda function to chose the keepX parameters of block.splsda (a.k.a mixDIABLO)
3- plot for perf objects displays the classification error rate w.r.t components
4- plot for tune objects displays the classification error rate w.r.t keepX values (not implemented for tune.block.splsda)
5- multilevel function has been removed (as planned) as it is now included as an argument in other functions (see pca, pls, splsda, etc)

1 – All tune functions (except for mixDIABLO/block.splsda module) include a ‘constraint’ argument to either build the model based on user input specific parameters (object$keepX.constraint) or based on the optimal parameter keepX determined by the tune function, see examples in help files.
2 – All perf functions (except for mixDIABLO/block.splsda module) have now a ‘constraint’ argument that allows the performances to be calculate either based on the number of parameters (object$keepX) defined in object or based on the variables selected on each component, see examples in help files.
3 – max.iter has been set to 100 to speed up computational time for all multivariate methods except pca/spca.
4 – cimDiablo: new arguments include transpose, row.names and col.names
5 – circosPlot: new arguments include var.names and comp. Argument ‘corThreshold’ has been replaced by ‘cutoff’.
6 – plotIndiv: new argument legend.title
7 – network function for block.spls(da) models and allows to plot for more than 2 blocks
8 – PCA: new argument ilr.offset to be used only for ILR log transform in PCA (mixMC module)
9 – Legend added in plotDiablo, new argument legend.ncol

Bug fixes:
1 – plotIndiv and ellipse: plot ellipse for all groups with more than 1 sample
2 – predict function: argument multilevel added, log transform included
3 – Call to from the RVAideMemoire package
4 – other small bugs as listed in out bitbucket issues, matching rgl package changes.

This entry was posted in Uncategorized, Updates. Bookmark the permalink.