A Two-Stage Approach to Maximize Interpretability of Drug Response Models Based on Multiple Molecular Data Types

A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016, ), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.


A two-stage regression method that can be used when various input data types are correlated, for example gene expression and methylation in drug response prediction. In the first stage it uses the upstream features (such as methylation) to predict the response variable (such as drug response), and in the second stage it uses the downstream features (such as gene expression) to predict the residuals of the first stage. In our manuscript (Aben et al., 2016), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.

The R package is available on CRAN.

News

TANDEM 1.0.2

Fixed a bug in relative.contributions() that decreased the relative contributions for correlated data types (by not taking into account the correlated part). Thanks to Wouter Touw for pointing this out!

TANDEM 1.0.1

Fixed a bug that occurred when using lambda.upstream="lambda.min" or lambda.downstream="lambda.min" in tandem(). All regression coefficients were correct, but the intercept was estimated using lambda.1se. This also affected results from predict() or nested.cv() using TANDEM fits where lambda.upstream="lambda.min" or lambda.downstream="lambda.min", negatively affecting the predictive performance.

In addition, I've added an option to set lambda="lambda.min" for the glmnet model in relative.contributions().

TANDEM 1.0.0

First release version!

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("TANDEM")

1.0.2 by Nanne Aben, a year ago


Browse source code at https://github.com/cran/TANDEM


Authors: Nanne Aben


Documentation:   PDF Manual  


GPL-2 license


Imports glmnet, Matrix

Suggests knitr, rmarkdown


See at CRAN