cn.mops (original) (raw)

This is the released version of cn.mops; for the devel version, seecn.mops.

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

Bioconductor version: Release (3.20)

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 [aut], Gundula Povysil [cre]

Maintainer: Gundula Povysil

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

Installation

To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("cn.mops")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("cn.mops")

Details

See More

Package Archives

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