Two-stage polytomous logistic regression (TOP): in this package, we developed a two-stage polytomous regression framework to handle cancer data with multivariate tumor characteristics. In the first stage, a standard polytomous model is used to specify for all subtypes defined by the cross-classification of different markers. In the second stage, the subtype-specific case-control odds ratios are specified using a more parsimonious model based on the case-control odds ratio for a baseline subtype, and the case-case parameters associated with tumor markers. Further, to reduce the degrees-of-freedom, we allow to specify case-case parameters for additional markers using a random-effect model.
The 'TOP' vignette will provide a good start point for using TOP package.
This R package is developed by Haoyu Zhang and William Wheeler, and maintained by Haoyu Zhang andrew.haoyu@gmail.com.
To install the development version of TOP, it's easiest to use the 'devtools' package.
install.packages("devtools")
library(devtools)
install_github("andrewhaoyu/TOP")
Zhang, Haoyu, et al. "A mixed-model approach for powerful testing of genetic associations with cancer risk incorporating tumor characteristics." Biostatistics 22.4 (2021): 772-788.