To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("fastseg")
In most cases, you don't need to download the package archive at all.
Bioconductor version: 2.14
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>
Citation (from within R,
enter citation("fastseg")
):
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R") biocLite("fastseg")
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("fastseg")
R Script | fastseg: Manual for the R package | |
Reference Manual |
biocViews | Classification, CopyNumberVariation, Software |
Version | 1.10.0 |
In Bioconductor since | BioC 2.9 (R-2.14) |
License | LGPL (>= 2.0) |
Depends | R (>= 2.13), GenomicRanges, Biobase |
Imports | graphics, stats, IRanges, BiocGenerics |
Suggests | DNAcopy, oligo |
System Requirements | |
URL | http://www.bioinf.jku.at/software/fastseg/fastseg.html |
Depends On Me | |
Imports Me | |
Suggests Me |
Follow Installation instructions to use this package in your R session.
Package Source | fastseg_1.10.0.tar.gz |
Windows Binary | fastseg_1.10.0.zip (32- & 64-bit) |
Mac OS X 10.6 (Snow Leopard) | fastseg_1.10.0.tgz |
Mac OS X 10.9 (Mavericks) | fastseg_1.10.0.tgz |
Browse/checkout source | (username/password: readonly) |
Package Downloads Report | Download Stats |
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