TANDEM

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, <doi:10.1093/bioinformatics/btw449>), we show that using TANDEM prevents the model from being dominated by gene expression and that the features selected by TANDEM are more interpretable.

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Description file content

Package
TANDEM
Type
Package
Title
A Two-Stage Approach to Maximize Interpretability of Drug Response Models Based on Multiple Molecular Data Types
Version
1.0.2
Date
2017-04-07
Author
Nanne Aben
Maintainer
Nanne Aben
Description
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.
Depends
R (>= 2.10)
Imports
glmnet, Matrix
License
GPL-2
LazyData
TRUE
RoxygenNote
6.0.1
Suggests
knitr, rmarkdown
VignetteBuilder
knitr
NeedsCompilation
no
Packaged
2017-06-15 09:59:17 UTC; nanne
Repository
CRAN
Date/Publication
2017-06-15 13:40:02 UTC

install.packages('TANDEM')

1.0.2

5 months ago

Nanne Aben

GPL-2

Depends on

R (>= 2.10)

Imports

glmnet, Matrix

Suggests

knitr, rmarkdown

Discussions