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' (Wang, Shixiang,
et al. (2020)
The goal of sigminer is to provide an uniform interface for genomic variation signature analysis and visualization.
sigminer is powered by NMF package and maftools package.
You can install the stable release of sigminer from CRAN with:
install.packages("sigminer")# OrBiocManager::install("sigminer")
You can install the development version of sigminer from Github with:
remotes::install_github("ShixiangWang/sigminer")
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).
and
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
pheatmap
to suggestget_cnlist
functionget_components
functiontest_run_components
functionsig_prepare
S3 methodsget_LengthFraction
functionsigminer
sig_get_similarity
functionsig_assign_samples
read_maf
sig_summarize_subtypes
function for summarize subtype datadraw_subtypes_comparison
function for plotting summarized data from sig_summarize_subtypes
functionsig_get_correlation
functiondraw_sig_corrplot
functionsubset.CopyNumber()
for subset CopyNumber objectgenome_measure
slot for CopyNumber objectNEWS.md
file to track changes to the package.