Introduction | Changes for MassArray in current BioC release | Optimal Amplicon Design | Conversion Controls | Data Import | Data Visualization | Single Nucleotide Polymorphism Detection | Previous Release Notes
Package: MassArray 1.65.0
Reid F. Thompson
MassArray: Analytical Tools for MassArray Data
This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom's MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.
Authors:
MassArray_1.65.0.tar.gz
MassArray_1.65.0.zip(r-4.7)MassArray_1.65.0.zip(r-4.6)MassArray_1.65.0.zip(r-4.5)
MassArray_1.65.0.tgz(r-4.6-any)MassArray_1.65.0.tgz(r-4.5-any)
MassArray_1.65.0.tar.gz(r-4.7-any)MassArray_1.65.0.tar.gz(r-4.6-any)
MassArray_1.65.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MassArray/json (API)
| # Install 'MassArray' in R: |
| install.packages('MassArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- MassArray.example.data - MassArray Data object
On BioConductor:MassArray-1.65.0(bioc 3.24)MassArray-1.64.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologydnamethylationsnpmassspectrometrygeneticsdataimportvisualization
Last updated from:36250c9022. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 160 | ||
| linux-devel-x86_64 | NOTE | 181 | ||
| source / vignettes | OK | 157 | ||
| linux-release-x86_64 | NOTE | 448 | ||
| macos-release-arm64 | NOTE | 81 | ||
| macos-oldrel-arm64 | NOTE | 86 | ||
| windows-devel | NOTE | 88 | ||
| windows-release | NOTE | 77 | ||
| windows-oldrel | NOTE | 123 | ||
| wasm-release | OK | 84 |
Exports:ampliconPredictionanalyzeCpGsbisConvertcalcMethcalcMWcalcPercentAdductcalcPercentConversioncombineconvControlcountCGscreateWiggleestimatePrimerDimerevaluateSNPsexpandSequencefindCollisionsfindFragmentsfindPeaksidentifySNPsimportEpiTyperDataimportEpiTyperData.newinSilicoFragmentationisAssayablenumCollisionsplot.MassArrayDatapositionposition<-revComplementrnaDigestsamplessamples<-sum.MassArraySpectrum
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Amplicon prediction | ampliconPrediction |
| Analyze CG methylation | analyzeCpGs |
| Bisulphite conversion | bisConvert |
| Calculate percent methylation | calcMeth |
| Calculate molecular weight | calcMW |
| Calculate percent salt adducts | calcPercentAdduct |
| Calculate percent conversion | calcPercentConversion |
| Combine MassArrayData objects | combine |
| Combine MassArrayData objects (methods) | combine,MassArrayData,MassArrayData-method combine,MassArrayData,missing-method combine-methods |
| Conversion control | convControl |
| Count number of CGs | countCGs |
| Create wiggle track | createWiggle |
| Estimate Primer Dimers | estimatePrimerDimer |
| Evaluate SNPs | evaluateSNPs |
| Expand nucleotide sequence | expandSequence |
| Find peak collisions | findCollisions |
| Find fragments | findFragments |
| Find peaks | findPeaks |
| Identify SNPs | identifySNPs |
| Import EpiTyper data (v.1.0) | importEpiTyperData |
| Import EpiTyper data (v.1.0.5) | importEpiTyperData.new |
| In silico fragmentation | inSilicoFragmentation |
| Is assayable? | isAssayable |
| MassArray Data object | MassArray.example.data |
| Class "MassArrayData" | $,MassArrayData-method $<-,MassArrayData-method initialize,MassArrayData-method MassArrayData-class [,MassArrayData-method |
| Class "MassArrayFragment" | $,MassArrayFragment-method $<-,MassArrayFragment-method initialize,MassArrayFragment-method MassArrayFragment-class |
| Class "MassArrayPeak" | $,MassArrayPeak-method $<-,MassArrayPeak-method initialize,MassArrayPeak-method MassArrayPeak-class |
| Class "MassArraySpectrum" | $,MassArraySpectrum-method $<-,MassArraySpectrum-method initialize,MassArraySpectrum-method MassArraySpectrum-class |
| Count peak collisions | numCollisions |
| Plot MassArrayData | plot.MassArrayData |
| Operate on positional information | position position<- |
| Operate on positional information (methods) | position,MassArrayData-method position-methods position<-,MassArrayData,character-method position<-,MassArrayData,missing-method |
| Reverse complement | revComplement |
| Reverse complement (methods) | revComplement,character-method revComplement,MassArrayData-method revComplement-methods |
| RNA digest | rnaDigest |
| Operate on sample name(s) | samples samples<- |
| Operate on sample name(s) (methods) | samples,MassArrayData-method samples-methods samples<-,MassArrayData,character-method samples<-,MassArrayData,missing-method |
| Sum MassArraySpectrum objects | sum.MassArraySpectrum |
