Package: CNAnorm 1.59.0
Stefano Berri
CNAnorm: A normalization method for Copy Number Aberration in cancer samples
Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.
Authors:
CNAnorm_1.59.0.tar.gz
CNAnorm_1.59.0.zip(r-4.7)CNAnorm_1.59.0.zip(r-4.6)CNAnorm_1.59.0.zip(r-4.5)
CNAnorm_1.59.0.tgz(r-4.6-x86_64)CNAnorm_1.59.0.tgz(r-4.6-arm64)CNAnorm_1.59.0.tgz(r-4.5-x86_64)CNAnorm_1.59.0.tgz(r-4.5-arm64)
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CNAnorm_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CNAnorm/json (API)
NEWS
| # Install 'CNAnorm' in R: |
| install.packages('CNAnorm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- CN - A CNAnorm object with information about most abundant ploidy states, obtained from data LS041.
- gPar - An object with the default graphical parameters
- hg19_hs_ideogr - An object with the ideogram information for homo sapiens - hg19
- LS041 - Mapped reads in tumor and matched blood for patient LS041
On BioConductor:CNAnorm-1.59.0(bioc 3.24)CNAnorm-1.58.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
copynumbervariationsequencingcoveragenormalizationwholegenomednaseqgenomicvariation
Last updated from:48ad80c66d. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 130 | ||
| linux-devel-arm64 | NOTE | 121 | ||
| linux-devel-x86_64 | NOTE | 181 | ||
| source / vignettes | OK | 157 | ||
| linux-release-arm64 | NOTE | 153 | ||
| linux-release-x86_64 | NOTE | 161 | ||
| macos-release-arm64 | NOTE | 126 | ||
| macos-release-x86_64 | NOTE | 295 | ||
| macos-oldrel-arm64 | NOTE | 102 | ||
| macos-oldrel-x86_64 | NOTE | 228 | ||
| windows-devel | NOTE | 119 | ||
| windows-release | NOTE | 92 | ||
| windows-oldrel | NOTE | 126 | ||
| wasm-release | OK | 87 |
Exports:addDNACopyaddSmootharmschrschrs<-CNAnormWorkflowdataFrame2objectdiscreteNormexportTablegcNormpeakPloidyplotGenomeplotPeakspospos<-ratioratio.nratio.sratio.s.nsegMeansegMean.nsugg.peakssugg.ploidyvalid.peaksvalid.ploidyvalidation
Dependencies:DNAcopy
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Methods for Function addDNACopy in Package `CNAnorm' | addDNACopy addDNACopy,CNAnorm-method addDNACopy-methods |
| Methods for Function addSmooth in Package `CNAnorm' | addSmooth addSmooth,CNAnorm-method addSmooth-methods |
| Accessors methods for Function ratio in Package `CNAnorm' | arms arms,CNAnorm-method arms-methods chrs chrs-methods chrs<- chrs<--methods pos pos,CNAnorm-method pos-methods pos<- pos<--methods |
| A CNAnorm object with information about most abundant ploidy states, obtained from data LS041. | CN |
| Class "CNAnorm" | chrs,CNAnorm-method chrs<-,CNAnorm-method CNAnorm CNAnorm-class length,CNAnorm-method pos<-,CNAnorm-method ratio,CNAnorm-method ratio.n,CNAnorm-method ratio.s,CNAnorm-method ratio.s.n,CNAnorm-method segMean,CNAnorm-method segMean.n,CNAnorm-method sugg.peaks,CNAnorm-method sugg.ploidy,CNAnorm-method valid.peaks,CNAnorm-method valid.ploidy,CNAnorm-method [,CNAnorm-method |
| Wrapper to '"CNAnorm"' workflow | CNAnormWorkflow |
| Convert a data frame into an object of Class '"CNAnorm"' | dataFrame2object |
| Class "DerivData" | DerivData-class length,DerivData-method |
| Methods for Function addSmooth in Package `CNAnorm' | discreteNorm discreteNorm,CNAnorm-method discreteNorm-methods |
| Methods for Function exportTable in Package `CNAnorm' | exportTable exportTable,CNAnorm-method exportTable-methods |
| Methods for Function gcNorm in Package `CNAnorm' | gcNorm gcNorm,CNAnorm-method gcNorm-methods |
| An object with the default graphical parameters | gPar |
| An object with the ideogram information for homo sapiens - hg19 | hg19_hs_ideogr |
| Class "InData" ~~~ | InData-class length,InData-method |
| Mapped reads in tumor and matched blood for patient LS041 | LS041 |
| Class "Params" | Params-class |
| Methods for Function peakPloidy in Package `CNAnorm' | peakPloidy peakPloidy,CNAnorm-method peakPloidy-methods |
| Methods for Function plotGenome in Package `CNAnorm' | plotGenome plotGenome,CNAnorm-method plotGenome-methods |
| Methods for Function plotPeaks in Package `CNAnorm' | plotPeaks plotPeaks,CNAnorm-method plotPeaks-methods |
| Methods for Function ratio in Package `CNAnorm' | ratio ratio-methods ratio.n ratio.n-methods ratio.s ratio.s-methods ratio.s.n ratio.s.n-methods segMean segMean-methods segMean.n segMean.n-methods |
| Methods for Function to retrieve suggested/validated ploidy and peaks in Package `CNAnorm' | sugg.peaks sugg.peaks-methods sugg.ploidy sugg.ploidy-methods valid.peaks valid.peaks-methods valid.ploidy valid.ploidy-methods |
| Methods for Function addSmooth in Package `CNAnorm' | validation validation,CNAnorm-method validation-methods |