Genomic alterations including single nucleotide substitution,
copy number alteration, etc. are the major force for cancer
initialization and development. Due to the specificity of molecular
lesions caused by genomic alterations, we can generate characteristic
alteration spectra, called 'signature' (Alexandrov, Ludmil B., et al. (2020)
The goal of sigminer is to provide an uniform interface for genomic variation signature analysis and visualization.
You can install the stable release of sigminer from CRAN with:
You can install the development version of sigminer from Github with:
If you use sigminer in academic field, please cite:
Wang, Shixiang, et al. "The predictive power of tumor mutational burden in lung cancer immunotherapy response is influenced by patients' sex." International journal of cancer (2019).
Gaujoux, Renaud, and Cathal Seoighe. "A Flexible R Package for Nonnegative Matrix Factorization."" BMC Bioinformatics 11, no. 1 (December 2010).
The code for extracting copy number signatures was based in part on the source code from paper Copy number signatures and mutational processes in ovarian carcinoma, if you use this feature, please also cite:
Macintyre, Geoff, et al. "Copy number signatures and mutational processes in ovarian carcinoma." Nature genetics 50.9 (2018): 1262.
The code for extracting mutational signatures was based in part on the source code of the maftools package, if you use this feature, please also cite:
Mayakonda, Anand, et al. "Maftools: efficient and comprehensive analysis of somatic variants in cancer." Genome research 28.11 (2018): 1747-1756.
MIT © 2019 Shixiang Wang, Geoffrey Macintyre, Xue-Song Liu
sig_summarize_subtypesfunction for summarize subtype data
draw_subtypes_comparisonfunction for plotting summarized data from
subset.CopyNumber()for subset CopyNumber object
genome_measureslot for CopyNumber object
NEWS.mdfile to track changes to the package.