CopyClust

A Copy-Number-Based Integrative Cluster Classification Scheme for Breast Cancer Samples

Installation

The CopyClust package can be installed in R:

 devtools::install_github("camyoung54/CopyClust")

Documentation

This package serves as an alternative to the iC10 package developed by Rueda et al. for the classification of breast cancer samples into integrative clusters when gene expression data is unavailable. CopyClust implements an XGBoost-based classifier trained on the copy number profiles of the METABRIC cohort to predict integrative cluster label based on copy number data alone. The iC10 package can be downloaded from CRAN:

install.packages("iC10")
library(iC10)

Example

The package contains a sample data set that can be used to explore how the package works:

formatted_data = CC_format(test_data_raw)
IntClust_labels = CopyClust(formatted_data)

Authors

• Cameron Young

License

MIT

References

• Curtis et al., The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups, (2012).
• Ali et al., Genome-driven integrated classification of breast cancer validated in over 7,500 samples, (2014).