Package: CGHbase 1.67.0
Mark van de Wiel
CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.
Contains functions and classes that are needed by arrayCGH packages.
Authors:
CGHbase_1.67.0.tar.gz
CGHbase_1.67.0.zip(r-4.5)CGHbase_1.67.0.zip(r-4.4)CGHbase_1.67.0.zip(r-4.3)
CGHbase_1.67.0.tgz(r-4.4-any)CGHbase_1.67.0.tgz(r-4.3-any)
CGHbase_1.67.0.tar.gz(r-4.5-noble)CGHbase_1.67.0.tar.gz(r-4.4-noble)
CGHbase_1.67.0.tgz(r-4.4-emscripten)CGHbase_1.67.0.tgz(r-4.3-emscripten)
CGHbase.pdf |CGHbase.html✨
CGHbase/json (API)
| # Install 'CGHbase' in R: |
| install.packages('CGHbase', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tgac-vumc/cghbase/issues
- Wilting - Cervical cancer arrayCGH data
- WiltingCalled - Cervical cancer arrayCGH data called with CGHcall
- WiltingNorm - Normalized log2 ratios from cervical cancer arrayCGH data.
- WiltingRaw - Raw log2 ratios from cervical cancer arrayCGH data.
- WiltingRegions - Regions of cervical cancer arrayCGH data as defined by CGHregions
- WiltingSeg - Segmented log2 ratios from cervical cancer arrayCGH data.
On BioConductor:CGHbase-1.65.0(bioc 3.20)CGHbase-1.64.0(bioc 3.19)
infrastructuremicroarraycopynumbervariation
Last updated 26 days agofrom:2905ae79c4. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 30 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 30 2024 |
| R-4.4-mac | NOTE | Oct 30 2024 |
| R-4.3-win | NOTE | Oct 30 2024 |
| R-4.3-mac | NOTE | Oct 30 2024 |
Exports:avedistbpendbpstartcallscalls<-chromosomescopynumbercopynumber<-frequencyPlotfrequencyPlotCallsinitializemake_cghRawncloneplotplot.cghCallplot.cghRawplot.cghRegionsplot.cghSegprobampprobamp<-probdlossprobdloss<-probgainprobgain<-problossprobloss<-probnormprobnorm<-regionsregions<-segmentedsegmented<-summaryPlot
Dependencies:BiobaseBiocGenericslimmamarraystatmod
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CGHbase: Base functions and classes for arrayCGH data analysis. | CGHbase-package CGHbase |
| Retrieve regions information from cghRegions object. | avedist nclone |
| Class to contain and describe called array comparative genomic hybridization data. | bpend,cghCall-method bpstart,cghCall-method calls,cghCall-method calls<-,cghCall,matrix-method cghCall cghCall-class chromosomes,cghCall-method class:cghCall copynumber,cghCall-method copynumber<-,cghCall,matrix-method frequencyPlotCalls,cghCall,missing-method initialize,cghCall-method plot,cghCall,missing-method plot.summary,cghCall,missing-method probamp,cghCall-method probamp<-,cghCall,matrix-method probdloss,cghCall-method probdloss<-,cghCall,matrix-method probgain,cghCall-method probgain<-,cghCall,matrix-method probloss,cghCall-method probloss<-,cghCall,matrix-method probnorm,cghCall-method probnorm<-,cghCall,matrix-method segmented,cghCall-method segmented<-,cghCall,matrix-method |
| Class to contain and describe raw or normalized array comparative genomic hybridization data. | bpend,cghRaw-method bpstart,cghRaw-method cghRaw cghRaw-class chromosomes,cghRaw-method class:cghRaw copynumber,cghRaw-method copynumber<-,cghRaw,matrix-method initialize,cghRaw-method plot,cghRaw,missing-method |
| Class to contain and describe array comparative genomic hybridization regions data. | avedist,cghRegions-method bpend,cghRegions-method bpstart,cghRegions-method cghRegions cghRegions-class chromosomes,cghRegions-method class:cghRegions frequencyPlot,cghRegions,missing-method initialize,cghRegions-method nclone,cghRegions-method plot.cghRegions,cghRegions,missing-method regions,cghRegions-method regions<-,cghRegions,matrix-method |
| Class to contain and describe segmented array comparative genomic hybridization data. | bpend,cghSeg-method bpstart,cghSeg-method cghSeg cghSeg-class chromosomes,cghSeg-method class:cghSeg copynumber,cghSeg-method copynumber<-,cghSeg,matrix-method initialize,cghSeg-method plot,cghSeg,missing-method segmented,cghSeg-method segmented<-,cghSeg,matrix-method |
| Retrieve feature position data from cgh objects. | bpend bpstart chromosomes |
| Retrieve copynumber data from cgh objects. | calls calls<- copynumber copynumber<- segmented segmented<- |
| Visualization of aCGH regions. | frequencyPlot |
| Visualization of aCGH profiles. | frequencyPlotCalls |
| Convert a dataframe or textfile to an object of class cghRaw. | make_cghRaw |
| Plot aCGH data. | plot.cghCall plot.cghRaw plot.cghRegions plot.cghSeg |
| Retrieve call probabilities from a cghCall object. | probamp probamp<- probdloss probdloss<- probgain probgain<- probloss probloss<- probnorm probnorm<- |
| Retrieve regions data from cghRegions object. | regions regions<- |
| Visualization of aCGH profiles. | summaryPlot |
| Cervical cancer arrayCGH data | Wilting |
| Cervical cancer arrayCGH data called with CGHcall | WiltingCalled |
| Normalized log2 ratios from cervical cancer arrayCGH data. | WiltingNorm |
| Raw log2 ratios from cervical cancer arrayCGH data. | WiltingRaw |
| Regions of cervical cancer arrayCGH data as defined by CGHregions | WiltingRegions |
| Segmented log2 ratios from cervical cancer arrayCGH data. | WiltingSeg |
