fastseg

DOI: 10.18129/B9.bioc.fastseg    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see fastseg.

fastseg - a fast segmentation algorithm

Bioconductor version: 3.8

fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments' first and higher order moments.

Author: Guenter Klambauer

Maintainer: Guenter Klambauer <fastseg at bioinf.jku.at>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("fastseg")

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("fastseg")

 

PDF	R Script	fastseg: Manual for the R package
PDF		Reference Manual

Details

biocViews	Classification, CopyNumberVariation, Software
Version	1.28.0
In Bioconductor since	BioC 2.9 (R-2.14) (7.5 years)
License	LGPL (>= 2.0)
Depends	R (>= 2.13), GenomicRanges, Biobase
Imports	methods, graphics, stats, BiocGenerics, S4Vectors, IRanges
LinkingTo
Suggests	DNAcopy, oligo
SystemRequirements
Enhances
URL	http://www.bioinf.jku.at/software/fastseg/fastseg.html
Depends On Me
Imports Me	methylKit
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	fastseg_1.28.0.tar.gz
Windows Binary	fastseg_1.28.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	fastseg_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/fastseg
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/fastseg
Package Short Url	http://bioconductor.org/packages/fastseg/
Package Downloads Report	Download Stats