ADaCGH2: Analysis of big data from aCGH experiments using parallel computing and ff objects
Version 2.16.0

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.

AuthorRamon 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>.
Bioconductor views CopyNumberVariants Microarray
Date of publicationNone
MaintainerRamon Diaz-Uriarte <rdiaz02@gmail.com>
LicenseGPL (>= 3)
Version2.16.0
URL https://github.com/rdiaz02/adacgh2
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ADaCGH2")

Popular 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...
See all...

All man pages Function index File listing

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...

Functions

BioHMMWrapper Source code
RAM.or.ff Source code
ad_FDRThres Source code
ad_HaarSeg Source code
ad_SegmentByPeaks Source code
add.names.as.attr Source code
break.and.write.vector Source code
buildIM Source code
caughtError Source code
caughtOtherError Source code
caughtOtherError.Web Source code
caughtOtherPackageError.Web Source code
caughtOurError2 Source code
caughtUserError2 Source code
cluster.clean.quit.Web Source code
createIM Source code
createIM2 Source code
createPage Source code
createTableArrChrom Source code
cutFile Man page Source code
daglad.ADa.1 Source code
distribute Source code
expungeNA Source code
ffListOut Source code
ffVecOut Source code
fig2dev Source code
gcmessage Source code
getCGHValue Source code
getChromValue Source code
getNames Source code
getOutValue Source code
getOutValueRAM3 Source code
getffObj Source code
getffObjNoOpen Source code
hmmWrapper Source code
imCircle Source code
imClose Source code
imClose3 Source code
imDefault Source code
imPoint Source code
imPoly Source code
imRect Source code
imText Source code
imagemap Source code
imagemap3 Source code
inpungeNA Source code
inputEx Man page
inputEx-sp Man page
inputEx.nona Man page
inputToADaCGH Man page Source code
internalBioHMM Source code
internalCGHseg Source code
internalChromPlot Source code
internalDNAcopy Source code
internalDNAcopySegm Source code
internalDNAcopySmooth Source code
internalGLAD Source code
internalHMM Source code
internalHaarSeg Source code
internalMADCall Source code
internalMerge Source code
internalWaveHsu Source code
is.wholeposnumber Source code
lines.imCircle Source code
lines.imDefault Source code
lines.imPoly Source code
lines.imRect Source code
lines.imagemap Source code
mcc Source code
moHTML Source code
mydcat Source code
mydcat2 Source code
mydcat3 Source code
mysize Source code
na.handle.ff Source code
namesff Source code
nfields.one.line Source code
nlines.to.skip.and.nf Source code
nodeWhere Source code
nominal.thresh Source code
our.hybrid Source code
our.sure Source code
ourMerge Source code
outToffdf Source code
outToffdf2 Source code
outputToCGHregions Man page Source code
pChromPlot Man page Source code
pSegment Man page
pSegmentBioHMM Man page Source code
pSegmentCGHseg Man page Source code
pSegmentDNAcopy Man page Source code
pSegmentGLAD Man page Source code
pSegmentHMM Man page Source code
pSegmentHaarSeg Man page Source code
pSegmentWavelets Man page Source code
piccardsKO Source code
piccardsStretch01 Source code
plt2fig Source code
print.imagemap Source code
puttogetherCGHseg Source code
read.data.column Source code
read.this.column Source code
segmentW Source code
setColClasses Source code
sizesobj Source code
stop.na.inf Source code
tempdir2 Source code
the.time.with.ms Source code
the.time.with.sec Source code
toHTML Source code
toHTML.default Source code
toHTML.imCircle Source code
toHTML.imDefault Source code
toHTML.imPoly Source code
toHTML.imRect Source code
toHTML.imText Source code
toHTML.imagemap Source code
usr2dev Source code
usr2plt Source code
usr2png Source code
vectorForArray Source code
vectorForArrayL2 Source code
vectorForArrayRAM Source code
vectorForArrayRAM2 Source code
vectorFromffList Source code
vectorFromffList2 Source code
warn.too.few.in.chrom Source code
warn.too.few.in.chrom2 Source code
wrapCreateTableArrChr Source code
xytrans Source code
xytrans2 Source code

Files

DESCRIPTION
NAMESPACE
R
R/ADaCGH-2.R
R/HaarSeg.R
R/imagemap.R
README.code.authors
build
build/vignette.rds
data
data/inputEx-sp.txt
data/inputEx.RData
data/inputEx.txt
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/ADaCGH2-long-examples.pdf
inst/doc/ADaCGH2.R
inst/doc/ADaCGH2.Rnw
inst/doc/ADaCGH2.pdf
inst/doc/benchmarks.pdf
inst/doc/index.html
inst/example-datadir
inst/example-datadir/Chrom.txt
inst/example-datadir/ID.txt
inst/example-datadir/Pos.txt
inst/example-datadir/col_4.txt
inst/example-datadir/col_5.txt
inst/example-datadir/col_6.txt
inst/example-datadir/col_7.txt
inst/example-datadir/col_8.txt
inst/example-datadir/col_9.txt
inst/imagemap-example
inst/imagemap-example/README-usage-Python-for-HTML-with-maps.txt
inst/imagemap-example/toMap.py
inst/imagemap-example/toMapMod.py
inst/sources-tex-Rnw-other
inst/sources-tex-Rnw-other/ADaCGH2-long-examples.R
inst/sources-tex-Rnw-other/ADaCGH2-long-examples.Rnw
inst/sources-tex-Rnw-other/README-sources-tex-Rnw-other
inst/sources-tex-Rnw-other/anal-benchmark-fig.pdf
inst/sources-tex-Rnw-other/anal-coleonyx.tex
inst/sources-tex-Rnw-other/anal-gallotia.tex
inst/sources-tex-Rnw-other/anal-lacerta-gallotia.tex
inst/sources-tex-Rnw-other/anal-lacerta.tex
inst/sources-tex-Rnw-other/benchmarks.bib
inst/sources-tex-Rnw-other/benchmarks.tex
inst/sources-tex-Rnw-other/read-coleonyx.tex
inst/sources-tex-Rnw-other/read-gallotia.tex
inst/sources-tex-Rnw-other/read-lacerta.tex
inst/sources-tex-Rnw-other/reading-benchmark-fig.pdf
man
man/cutFile.Rd
man/inputEx.Rd
man/inputToADaCGH.Rd
man/outputToCGHregions.Rd
man/pChromPlot.Rd
man/pSegment.Rd
src
src/all_headers.h
src/init.c
src/r_haarseg.c
vignettes
vignettes/ADaCGH2.Rnw
vignettes/ADaCGH2.bib
ADaCGH2 documentation built on May 20, 2017, 10:58 p.m.

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