Package: CNAnorm 1.53.0
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:
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CNAnorm.pdf |CNAnorm.html✨
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.
- LS041 - Mapped reads in tumor and matched blood for patient LS041
- gPar - An object with the default graphical parameters
- hg19_hs_ideogr - An object with the ideogram information for homo sapiens - hg19
On BioConductor:CNAnorm-1.53.0(bioc 3.21)CNAnorm-1.52.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
copynumbervariationsequencingcoveragenormalizationwholegenomednaseqgenomicvariationfortran
Last updated 2 months agofrom:65ad3483dd. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 29 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 29 2024 |
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 |