This vignette | Overview: | The data for all the examples | Example 1: RAM objects and forking | Example 2: ff objects and cluster | Example 3: ff objects and forking | Input and output to/from other packages | Why ADaCGH2 instead of a ``manual'' solution | Session info and packages used
Package: ADaCGH2 2.53.0
Ramon Diaz-Uriarte
ADaCGH2: Analysis of Big Data from aCGH Experiments using Parallel Computing and ff Objects
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, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Authors:
ADaCGH2_2.53.0.tar.gz
ADaCGH2_2.53.0.zip(r-4.7)ADaCGH2_2.53.0.zip(r-4.6)ADaCGH2_2.53.0.zip(r-4.5)
ADaCGH2_2.53.0.tgz(r-4.6-x86_64)ADaCGH2_2.53.0.tgz(r-4.6-arm64)ADaCGH2_2.53.0.tgz(r-4.5-x86_64)ADaCGH2_2.53.0.tgz(r-4.5-arm64)
ADaCGH2_2.53.0.tar.gz(r-4.7-arm64)ADaCGH2_2.53.0.tar.gz(r-4.7-x86_64)ADaCGH2_2.53.0.tar.gz(r-4.6-arm64)ADaCGH2_2.53.0.tar.gz(r-4.6-x86_64)
ADaCGH2_2.53.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ADaCGH2/json (API)
| # Install 'ADaCGH2' in R: |
| install.packages('ADaCGH2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rdiaz02/adacgh2/issues
Datasets:
- inputEx - A fictitious aCGH data set
- inputEx-sp - A fictitious aCGH data set
On BioConductor:ADaCGH2-2.53.0(bioc 3.24)ADaCGH2-2.52.0(bioc 3.23)
microarraycopynumbervariationacgh
Last updated from:4432814e44. Checks:1 WARNING, 13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 189 | ||
| linux-devel-arm64 | OK | 259 | ||
| linux-devel-x86_64 | OK | 333 | ||
| source / vignettes | OK | 298 | ||
| linux-release-arm64 | OK | 264 | ||
| linux-release-x86_64 | OK | 349 | ||
| macos-release-arm64 | OK | 256 | ||
| macos-release-x86_64 | OK | 411 | ||
| macos-oldrel-arm64 | OK | 199 | ||
| macos-oldrel-x86_64 | OK | 449 | ||
| windows-devel | OK | 220 | ||
| windows-release | OK | 238 | ||
| windows-oldrel | OK | 226 | ||
| wasm-release | OK | 134 |
Exports:cutFileinputToADaCGHoutputToCGHregionspChromPlotpSegmentCGHsegpSegmentDNAcopypSegmentGLADpSegmentHaarSegpSegmentHMMpSegmentWavelets
Dependencies:aCGHaffyaffyioannotateAnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemcliclustercpp11crayoncurlDBIDNAcopyfarverfastmapffgenefiltergenericsggplot2gluegtablehttrIRangesisobandjsonliteKEGGRESTlabelinglatticelifecyclelimmaMASSMatrixMatrixGenericsmatrixStatsmemoisemimemultitapermulttestopensslpixmappkgconfigpngpreprocessCoreR6RColorBrewerrlangRSQLiteS4VectorsS7sandwichscalesSeqinfostatmodstrucchangesurvivalsystilingArrayvctrsviridisLitevsnwaveslimwithrXMLxtableXVectorzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Cut a file and return individual columns | cutFile |
| A fictitious aCGH data set | inputEx inputEx-sp inputEx.nona |
| Convert CGH data to ff or RAM objects for use with ADaCGH2 | inputToADaCGH |
| ADaCGH2 output as input to CGHregions | outputToCGHregions |
| Segment plots for aCGH as PNG | pChromPlot |
| Parallelized/"unified" versions of several aCGH segementation algorithms/methods | pSegment pSegmentCGHseg pSegmentDNAcopy pSegmentGLAD pSegmentHaarSeg pSegmentHMM pSegmentWavelets |
