TitanCNA

TitanCNA a R/Bioconductor package for analyzing subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in whole genome and exome sequencing of tumours.

Ha, G., et al. (2014). TITAN: Inference of copy number architectures in clonal cell populations from tumour whole genome sequence data. Genome Research, 24: 1881-1893. (PMID: 25060187)

Contact

Gavin Ha
Dana-Farber Cancer Institute
Broad Institute
contact: gavinha@gmail.com or gavinha@broadinstitute.org
Date: May 13, 2017

Links
News
Installation
Usage
Vignette in TitanCNA R package
Acknowledgements
License

Links

TitanCNA GitHub: https://github.com/gavinha/TitanCNA
KRONOS TITAN Workflow: https://github.com/MO-BCCRC/titan_workflow
Google Groups: https://groups.google.com/forum/#!forum/titancna
TitanCNA website: http://compbio.bccrc.ca/software/titan/
Publication in Genome Research: http://genome.cshlp.org/content/24/11/1881

News

(See NEWS for previous version notes)

TitanCNA version 1.15.0 changes

10X Genomics analysis

Please see scripts for instructions on running the 10X Genomics analysis.

New script to help select optimal solutions. Please see scripts/R_scripts
Added snakemake pipeline for entire TITAN workflow. Please see scripts/snakemake.
New function

plotSegmentMedians()
loadHaplotypeAlleleCounts(): loads input allele counts with phasing information
plotHaplotypeFraction(): results from 10X Genomics WGS data with phasing of haplotype blocks

Modified features (no changes for user-accessible functions)

updateParameters: coordinate descent estimate of ploidy update uses previously estimated normal parameter from the same corodinate descent iteration ; leads to faster convergence

Installation

Install TitanCNA R package from github

From within R-3.3.2 or higher,

install.packages("devtools")
library(devtools)
install_github("gavinha/TitanCNA")

Install TitanCNA from Bioconductor

From within R-3.3.2 or higher,

source("https://bioconductor.org/biocLite.R")
biocLite("TitanCNA")

Install other dependencies

Install the HMMcopy suite Please follow instructions on the HMMcopy website http://compbio.bccrc.ca/software/hmmcopy/.
KRONOS TITAN Workflow The easiest way to generate these files is by using the downloadable pipeline from https://github.com/MO-BCCRC/titan_workflow.

Usage

R scripts are provided to run the R component of the TITAN analysis using the TitanCNA R/Bioconductor package.
Please go to the scripts directory and look at the README there for more details.

Vignette in TitanCNA R package

The PDF of the vignette can be accessed from R

library(TitanCNA)
browseVignettes(package = "TitanCNA")

The path of the file can also be located using

pathToInstall <- system.file(package = "TitanCNA")
pathToPdf <- paste0(pathToInstall, "/int/doc/TitanCNA.pdf)

The example provided will reproduce Figure 1 in the manuscript. However, it will be slightly different because the example is only based on the analysis of chr2, not genome-wide.

Acknowledgements

TitanCNA was developed by Gavin Ha while in the laboratories of Sohrab Shah (sshah@bccrc.ca) and Sam Aparicio (saparicio@bccrc.ca) at the Dept of Molecular Oncology, BC Cancer Agency, Vancouver, Canada.
Yikan Wang and Daniel Lai have contributed code and discussions to this project.
The KRONOS TITAN workflow was developed by Diljot Grewal (dgrewal@bccrc.ca) and Jafar Taghiyar (jtaghiyar@bccrc.ca).
HMMcopy was co-developed by Daniel Lai and Gavin Ha.

TitanCNA was inspired by existing methods including OncoSNP and PyClone

Software License

TitanCNA R code is open source and is R/Bioconductor package is under GPLv3. This applies to the v1.9.0 and all subsequent versions within and obtained from Bioconductor.
Users who are using TitanCNA earlier than v1.9.0 not for the purpose of academic research should contact gavinha@broadinstitute.org, sshah@bccrc.ca, and prebstein@bccancer.bc.ca to inquire about previous licensing.

haoziyeung/TitanCNA