MADSEQ

Welcome to R/MADSEQ.

MADSEQ is an R package designed for mosaic aneuploidy detection and quantification using next generation sequencing data. MADSEQ package contains a group of hierarchical Bayesian models for the detection of different types of mosaic aneuploidy. These models use Markov Chain Monte Carlo method to sample posterior distribution for different parameters related to mosaic aneuploidy.

The MADSEQ package can be used for the following purpose:

• Sensitive detection of mosaic aneuploidy
• Quantification of the level of mosaic aneuploidy
• Inference of the origin of aneuploidy

Dependencies

• R (latest version)
• JAGS installed on your computer
• R package: rjags, visit their cran page or github for the instruction to install it.

Installation

The package could be installed by:

1. Download TAR, and install it in R by:

install.packages("directory_to_the_downloaded_package/file_name_MADSEQ.tar.gz")

1. Install it from github using devtools:

library(devtools)
install_github("ykong2/MADSEQ", build_vignettes=TRUE)

User Guide

The documentation of MADSEQ package can be found here. Please follow the instructions for the data preparation, model application and analysis.

Contact

For help, new feature request or report bug regarding MADSEQ package, please contact at yu.kong@phd.einstein.yu.edu.