Capture Genomic Variation Signatures using Non-Negative Matrix Factorization

Contains functions for identification of copy number signatures (Geoffrey et al. (2018) ) and mutation signatures (Alexandrov et al. (2013) ) by non-negative matrix factorization, signature analysis and visualization. It can be used to capture signatures of genomic variation, compare genotype or phenotype features of different signatures and thus uncover the relationship between the mechanism of genomic variation and phenotypes in cancer.


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Overview

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.

Installation

You can install the stable release of sigminer from CRAN with:

install.packages("sigminer")
# Or
BiocManager::install("sigminer")

You can install the development version of sigminer from Github with:

remotes::install_github("ShixiangWang/sigminer")

Citation

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).

Acknowledgments

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.

LICENSE

MIT © 2019 Shixiang Wang, Geoffrey Macintyre, Xue-Song Liu

News

sigminer v0.1.11

  • fix #11

sigminer v0.1.10

  • correct year for \doi{10.1038/nature12477}
  • fix #9

sigminer v0.1.9

  • add pheatmap to suggest

sigminer v0.1.8

  • promote get_cnlist function
  • support setting individual component numbers for each feature in get_components function
  • add test_run_components function
  • update author list
  • add package site

sigminer v0.1.7

  • try submitting to CRAN

sigminer v0.1.6

  • update readme & citation & authors
  • export sig_prepare S3 methods
  • promote speed of get_LengthFraction function

sigminer v0.1.5

  • update introduction for package sigminer
  • fix text problem provided by CRAN check team
  • add sig_get_similarity function
  • add toy datasets & update examples
  • fix typo in sig_assign_samples
  • export read_maf
  • update README

sigminer v0.1.4

  • add examples for all exported functions

sigminer v0.1.3

  • add sig_summarize_subtypes function for summarize subtype data
  • add draw_subtypes_comparison function for plotting summarized data from sig_summarize_subtypes function

sigminer v0.1.2

  • add sig_get_correlation function
  • add draw_sig_corrplot function

sigminer v0.1.1

  • add subset.CopyNumber() for subset CopyNumber object
  • add genome_measure slot for CopyNumber object

sigminer v0.1.0

  • Added a NEWS.md file to track changes to the package.
  • Finish basic functions, including
    • read data
    • prepare data
    • estimate signature number
    • extract signatures
    • plot copy number profile
    • plot signature profile
    • plot signature activity
    • ...

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("sigminer")

0.1.11 by Shixiang Wang, 2 months ago


https://github.com/ShixiangWang/sigminer


Report a bug at https://github.com/ShixiangWang/sigminer/issues


Browse source code at https://github.com/cran/sigminer


Authors: Shixiang Wang [aut, cre] , Geoffrey Macintyre [ctb] , Xue-Song Liu [ctb]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports cluster, corrplot, cowplot, data.table, doParallel, dplyr, flexmix, foreach, ggplot2, maftools, methods, NMF, RColorBrewer, tidyr, magrittr, purrr

Suggests BSgenome, BSgenome.Hsapiens.UCSC.hg19, cowsay, ggpubr, knitr, rmarkdown, covr, testthat, prettydoc, pheatmap


See at CRAN