fastseg: fastseg - a fast segmentation algorithm

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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
Date of publication
None
Maintainer
Guenter Klambauer <fastseg@bioinf.jku.at>
License
LGPL (>= 2.0)
Version
1.20.0
URLs

View on Bioconductor

Man pages

coriell
Array CGH data set of Coriell cell lines
fastseg
Detection of breakpoints using a fast segmentation algorithm...
fastsegData
Example data set for fastseg
segPlot
Plots the data from a copy number array experiment (aCGH,...
toDNAcopyObj
Function to create a DNAcopy object for plot functions.

Files in this package

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