cn.mops

cn.mops - Mixture of Poissons for CNV detection in NGS data

Bioconductor version: 2.10

cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.

Author: Guenter Klambauer

Maintainer: Guenter Klambauer <cn.mops at bioinf.jku.at>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("cn.mops")

To cite this package in a publication, start R and enter:

    citation("cn.mops")

Documentation

PDF R Script cn.mops: Manual for the R package
PDF   Reference Manual

Details

biocViews Bioinformatics, CopyNumberVariants, HighThroughputSequencing, Sequencing, Software
Depends R (>= 2.14), BiocGenerics(>= 0.1.0), Biobase, IRanges, GenomicRanges(>= 1.7.8)
Imports methods, graphics, BiocGenerics, IRanges, Rsamtools,
Suggests snow, DNAcopy
System Requirements
License LGPL (>= 2.0)
URL http://www.bioinf.jku.at/software/cnmops/cnmops.html
Depends On Me
Imports Me
Suggests Me
Version 1.2.6
Since Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source cn.mops_1.2.6.tar.gz
Windows Binary cn.mops_1.2.6.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary cn.mops_1.2.6.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:

 

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center