This repository describes the model building processes and the validation steps for GenomicSuperSignature package. All the Figures and Tables in GenomicSuperSignature paper can be reproduced using the codes and instruction in this repository.
To run analyses under Results and Methods, we recommend to clone this
repository.
git clone [email protected]:shbrief/GenomicSuperSignaturePaper.git
You can download RAVmodels from Google bucket (it's free, FYI) using wget or
GenomicSuperSignature::getModel() function. Currently, two different
RAVmodels are available, annotated with different prior gene sets.
## Download the latest RAVmodel with wget
wget https://storage.googleapis.com/genomic_super_signature/RAVmodel_C2.rds
wget https://storage.googleapis.com/genomic_super_signature/RAVmodel_PLIERpriors.rds
## Download RAVmodel with GenomicSuperSignature::getModel function
BiocManager::install("GenomicSuperSignature")
getModel("C2")
getModel("PLIERpriors")
A few accessory functions to run examples in this repository can be accessed through GenomicSuperSignaturePaper package.
## Install GenomicSuperSignaturePaper
devtools::install_github("shbrief/GenomicSuperSignaturePaper")
You can check the available RAVmodels through availableRAVmodel function:
> GenomicSuperSignature::availableRAVmodel()
prior version update pkg_version
1 C2 beta 20201101 1.1.0
3 C2 latest 20220115 1.3.0
4 PLIERpriors beta 20201101 1.1.0
6 PLIERpriors latest 20220115 1.3.0