fastseg: fastseg - a fast segmentation algorithm

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("fastseg")
AuthorGuenter Klambauer
Bioconductor views Classification CopyNumberVariation
Date of publicationNone
MaintainerGuenter Klambauer <fastseg@bioinf.jku.at>
LicenseLGPL (>= 2.0)
Version1.22.0
http://www.bioinf.jku.at/software/fastseg/fastseg.html

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/fastseg.R R/roxygen.R R/segPlot.R R/toDnaCopy.R
build
build/vignette.rds
data
data/coriell.rda
data/fastsegData.rda
inst
inst/CITATION
inst/doc
inst/doc/fastseg.R
inst/doc/fastseg.Rnw
inst/doc/fastseg.pdf
man
man/coriell.Rd man/fastseg.Rd man/fastsegData.Rd man/segPlot.Rd man/toDNAcopyObj.Rd
src
src/R_init_fastseg.c
src/fastseg.h
src/segment.cpp
src/segmentCyberT.cpp
vignettes
vignettes/bioinf-article.txi
vignettes/bioinf-bar.png
vignettes/bioinf.cls
vignettes/fastseg.Rnw
vignettes/fastseg.bib

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