ADaCGH2: Analysis of big data from aCGH experiments using parallel computing and ff objects

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Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

Author
Ramon Diaz-Uriarte <rdiaz02@gmail.com> and Oscar M. Rueda <rueda.om@gmail.com>. Wavelet-based aCGH smoothing code from Li Hsu <lih@fhcrc.org> and Douglas Grove <dgrove@fhcrc.org>. Imagemap code from Barry Rowlingson <B.Rowlingson@lancaster.ac.uk>. HaarSeg code from Erez Ben-Yaacov; downloaded from <http://www.ee.technion.ac.il/people/YoninaEldar/Info/software/HaarSeg.htm>.
Date of publication
None
Maintainer
Ramon Diaz-Uriarte <rdiaz02@gmail.com>
License
GPL (>= 3)
Version
2.14.0
URLs

View on Bioconductor

Man pages

cutFile
Cut a file and return individual columns
inputEx
A fictitious aCGH data set
inputToADaCGH
Convert CGH data to ff or RAM objects for use with ADaCGH2
outputToCGHregions
ADaCGH2 output as input to CGHregions
pChromPlot
Segment plots for aCGH as PNG
pSegment
Parallelized/"unified" versions of several aCGH segementation...

Files in this package

ADaCGH2/DESCRIPTION
ADaCGH2/NAMESPACE
ADaCGH2/R
ADaCGH2/R/ADaCGH-2.R
ADaCGH2/R/HaarSeg.R
ADaCGH2/R/imagemap.R
ADaCGH2/README.code.authors
ADaCGH2/build
ADaCGH2/build/vignette.rds
ADaCGH2/data
ADaCGH2/data/inputEx-sp.txt
ADaCGH2/data/inputEx.RData
ADaCGH2/data/inputEx.txt
ADaCGH2/inst
ADaCGH2/inst/CITATION
ADaCGH2/inst/NEWS
ADaCGH2/inst/doc
ADaCGH2/inst/doc/ADaCGH2-long-examples.pdf
ADaCGH2/inst/doc/ADaCGH2.R
ADaCGH2/inst/doc/ADaCGH2.Rnw
ADaCGH2/inst/doc/ADaCGH2.pdf
ADaCGH2/inst/doc/benchmarks.pdf
ADaCGH2/inst/doc/index.html
ADaCGH2/inst/example-datadir
ADaCGH2/inst/example-datadir/Chrom.txt
ADaCGH2/inst/example-datadir/ID.txt
ADaCGH2/inst/example-datadir/Pos.txt
ADaCGH2/inst/example-datadir/col_4.txt
ADaCGH2/inst/example-datadir/col_5.txt
ADaCGH2/inst/example-datadir/col_6.txt
ADaCGH2/inst/example-datadir/col_7.txt
ADaCGH2/inst/example-datadir/col_8.txt
ADaCGH2/inst/example-datadir/col_9.txt
ADaCGH2/inst/imagemap-example
ADaCGH2/inst/imagemap-example/README-usage-Python-for-HTML-with-maps.txt
ADaCGH2/inst/imagemap-example/toMap.py
ADaCGH2/inst/imagemap-example/toMapMod.py
ADaCGH2/inst/sources-tex-Rnw-other
ADaCGH2/inst/sources-tex-Rnw-other/ADaCGH2-long-examples.R
ADaCGH2/inst/sources-tex-Rnw-other/ADaCGH2-long-examples.Rnw
ADaCGH2/inst/sources-tex-Rnw-other/README-sources-tex-Rnw-other
ADaCGH2/inst/sources-tex-Rnw-other/anal-benchmark-fig.pdf
ADaCGH2/inst/sources-tex-Rnw-other/anal-coleonyx.tex
ADaCGH2/inst/sources-tex-Rnw-other/anal-gallotia.tex
ADaCGH2/inst/sources-tex-Rnw-other/anal-lacerta-gallotia.tex
ADaCGH2/inst/sources-tex-Rnw-other/anal-lacerta.tex
ADaCGH2/inst/sources-tex-Rnw-other/benchmarks.bib
ADaCGH2/inst/sources-tex-Rnw-other/benchmarks.tex
ADaCGH2/inst/sources-tex-Rnw-other/read-coleonyx.tex
ADaCGH2/inst/sources-tex-Rnw-other/read-gallotia.tex
ADaCGH2/inst/sources-tex-Rnw-other/read-lacerta.tex
ADaCGH2/inst/sources-tex-Rnw-other/reading-benchmark-fig.pdf
ADaCGH2/man
ADaCGH2/man/cutFile.Rd
ADaCGH2/man/inputEx.Rd
ADaCGH2/man/inputToADaCGH.Rd
ADaCGH2/man/outputToCGHregions.Rd
ADaCGH2/man/pChromPlot.Rd
ADaCGH2/man/pSegment.Rd
ADaCGH2/src
ADaCGH2/src/all_headers.h
ADaCGH2/src/init.c
ADaCGH2/src/r_haarseg.c
ADaCGH2/vignettes
ADaCGH2/vignettes/ADaCGH2.Rnw
ADaCGH2/vignettes/ADaCGH2.bib