Package: funtooNorm 1.29.0
Kathleen Klein
funtooNorm: Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.
Authors:
funtooNorm_1.29.0.tar.gz
funtooNorm_1.29.0.zip(r-4.5)funtooNorm_1.29.0.zip(r-4.4)funtooNorm_1.29.0.zip(r-4.3)
funtooNorm_1.29.0.tgz(r-4.4-any)funtooNorm_1.29.0.tgz(r-4.3-any)
funtooNorm_1.29.0.tar.gz(r-4.5-noble)funtooNorm_1.29.0.tar.gz(r-4.4-noble)
funtooNorm_1.29.0.tgz(r-4.4-emscripten)funtooNorm_1.29.0.tgz(r-4.3-emscripten)
funtooNorm.pdf |funtooNorm.html✨
funtooNorm/json (API)
NEWS
| # Install 'funtooNorm' in R: |
| install.packages('funtooNorm', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:funtooNorm-1.29.0(bioc 3.20)funtooNorm-1.28.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationpreprocessingnormalization
Last updated 5 months agofrom:a406fc9898. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 28 2024 |
| R-4.5-win | WARNING | Sep 28 2024 |
| R-4.5-linux | WARNING | Sep 28 2024 |
| R-4.4-win | WARNING | Sep 28 2024 |
| R-4.4-mac | WARNING | Sep 28 2024 |
| R-4.3-win | WARNING | Sep 28 2024 |
| R-4.3-mac | WARNING | Sep 28 2024 |
Exports:agreementfromGenStudFilesfromRGChannelSetfuntooNormgetGRangesgetNormBetagetNormMgetRawBetagetSnpMplotValidationGraphshow
Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrfansifastmapforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueHDF5Arrayhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestilluminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplogrplsplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| funtooNorm | funtooNorm-package |
| Function to measure intra-replicate agreement for methylation data. | agreement |
| Creates a S4 object of class 'SampleSet' from GenomeStudio files | fromGenStudFiles |
| Creates an object of class SampleSet from a RGChannelSet minfi | fromRGChannelSet |
| The funtooNorm normalization function | funtooNorm funtooNorm,SampleSet-method |
| Build GRange object of methylation probes | getGRanges getGRanges,SampleSet-method |
| Computes Beta values from normalized signals | getNormBeta getNormBeta,SampleSet-method |
| Computes M values,log2(Meth/Unmeth), from normalized signals | getNormM getNormM,SampleSet-method |
| Computes Beta value from raw signals | getRawBeta getRawBeta,SampleSet-method |
| Computes M values after normalization of SNP data. | getSnpM getSnpM,SampleSet-method |
| plot of Validation Graph for determing number of components | plotValidationGraph plotValidationGraph,SampleSet-method |
| S4 class object SampleSet | SampleSet-class |
| Show Object SampleSet | show,SampleSet-method |
