VSHunter: Capture Variation Signatures from Genomic Data

This package retired, users should switch to R package sigminer

The goal of VSHunter is to capture variation signature from genomic data. For now, we decode copy number pattern from absolute copy number profile. This package collects R code from paper Copy number signatures and mutational processes in ovarian carcinoma and tidy them as a open source R package for bioinformatics community.

Before you use this tool, you have to obtain absolute copy number profile for samples via software like ABSOLUTE v2, QDNASeq etc..

Procedure

1. summarise copy-number profile using a number of different feature distributions:
   • Sgement size
   • Breakpoint number (per ten megabases)
   • change-point copy-number
   • Breakpoint number (per chromosome arm)
   • Length of segments with oscillating copy-number
2. apply mixture modelling to breakdown each feature distribution into mixtures of Gaussian or mixtures of Poisson distributions using the flexmix package.
3. generate a sample-by-component matrix representing the sum of posterior probabilities of each copy-number event being assigned to each component.
4. use NMF package to factorise the sample-by-component matrix into a signature-by-sample matrix and component-by signature-matrix.

Installation

You can install UCSCXenaTools from github with:

# install.packages("devtools")
devtools::install_github("ShixiangWang/VSHunter", build_vignettes = TRUE)

update features and function will show in vignettes in the future

Load package.

library(VSHunter)

Citation

• Macintyre, Geoff, et al. “Copy number signatures and mutational processes in ovarian carcinoma.” Nature genetics 50.9 (2018): 1262.

If you wanna thank my work for this package, you can also cite (and inlucde link of this package - https://github.com/ShixiangWang/VSHunter):

• Wang, Shixiang, et al. “APOBEC3B and APOBEC mutational signature as potential predictive markers for immunotherapy response in non-small cell lung cancer.” Oncogene (2018).