In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

VSHunter: Capture Variation Signatures from Genomic Data

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..

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  eval = FALSE
)

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.

knitr::include_graphics(path = "https://media.springernature.com/m685/springer-static/image/art%3A10.1038%2Fs41588-018-0179-8/MediaObjects/41588_2018_179_Fig1_HTML.png")

# devtools::load_all()
# library(flexmix)
# library(QDNAseq)
# library(NMF)
if(!require("VSHunter")){
  devtools::load_all()
}

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).

ShixiangWang/VSHunter documentation built on June 27, 2019, 4:56 p.m.