# VSHunter

**Repository Path**: ShixiangWang/VSHunter

## Basic Information

- **Project Name**: VSHunter
- **Description**: No description available
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2021-08-31
- **Last Updated**: 2024-05-30

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README


<!-- README.md is generated from README.Rmd. Please edit that file -->

# VSHunter: Capture Variation Signatures from Genomic Data

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**This package retired, users should switch to R package [**sigminer**](https://github.com/ShixiangWang/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](https://www.nature.com/articles/s41588-018-0179-8)* 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.

<img src="https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41588-018-0179-8/MediaObjects/41588_2018_179_Fig1_HTML.png" title="Copy number signature identification, Macintyre, Geoff, et al.(2018)" alt="Copy number signature identification, Macintyre, Geoff, et al.(2018)" style="display: block; margin: auto;" />

## Installation

You can install UCSCXenaTools from github with:

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

> update features and function will show in vignettes in the future

Load package.

``` r
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).*