2.1 Package prerequisite

All R package dependencies ofsigminer can be checked atspecific fields ofDESCRIPTION file.Of note, unlike common R package, many key features ofsigminer are only available when the suggested packages are installed.Most of them are fromBioconductor, so R packageBiocManager must be installedbefore installingsigminer. You have to useBiocManager instead ofinstall.packages() to installsigminer.If you want to handle other reference genome data excepthg19, e.g., forhg38, you also have to installBioconductorpackageBSgenome.Hsapiens.UCSC.hg38 before/after installingsigminer.

2.2 Package installation

The stable release version ofsigminer package can be installed from the CRAN:

install.packages("BiocManager")BiocManager::install("sigminer", dependencies=TRUE)

Setdependencies = TRUE is recommended because many packages are required for accessing full features provided bysigminer (we described this in previous section).The development version ofsigminer package can be installed from Github or Gitee after installing CRAN versionsigminer:

install.packages("remotes")# From GitHubremotes::install_github("ShixiangWang/sigminer", dependencies=TRUE)# From Giteeremotes::install_git("https://gitee.com/ShixiangWang/sigminer", dependencies=TRUE)

If you see notification of package update, please keep this package up to date.

Thesigminer is also available in Condaforge channel. If you are using Conda,you can installsigminer with:

# Please note version number of the bioconda release# You can install an individual environment firstly with# conda create -n sigminer# conda activate sigminerconda install-c bioconda-c conda-forge r-sigminer

2.3 Package loading

To load package, run:

library(sigminer)

More info aboutsigminer can be given as:

hello()## Thanks for using 'sigminer' package!## =========================================================================## Version: 2.1.1## Run citation('sigminer') to see how to cite sigminer in publications.#### Project home : https://github.com/ShixiangWang/sigminer## Bug report   : https://github.com/ShixiangWang/sigminer/issues## Documentation: https://shixiangwang.github.io/sigminer-book/## =========================================================================##

2.4 Package references

All datasets/functions are well organized and documented atpackagereferrence list.For checking usage of a specific functionfun, you can also run?fun in your R console.For example, to see usageread_copynumber()

library(sigminer)?read_copynumber