To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

cn.mops

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

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("cn.mops")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cn.mops")

 

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

Details

biocViews CellBiology, CopyNumberVariation, Genetics, HapMap, Homo_sapiens, Sequencing, Software
Version 1.10.1
In Bioconductor since BioC 2.9 (R-2.14)
License LGPL (>= 2.0)
Depends R (>= 2.12), BiocGenerics, Biobase, IRanges, GenomicRanges
Imports methods, graphics, BiocGenerics, IRanges, Rsamtools
Suggests snow, DNAcopy
System Requirements
URL http://www.bioinf.jku.at/software/cnmops/cnmops.html
Depends On Me
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source cn.mops_1.10.1.tar.gz
Windows Binary cn.mops_1.10.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) cn.mops_1.10.1.tgz
Mac OS X 10.9 (Mavericks) cn.mops_1.10.1.tgz
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