Package: wateRmelon 2.13.0
Leo C Schalkwyk
wateRmelon: Illumina DNA methylation array normalization and metrics
15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.
Authors:
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wateRmelon.pdf |wateRmelon.html✨
wateRmelon/json (API)
| # Install 'wateRmelon' in R: |
| install.packages('wateRmelon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- coef - Age Prediction from methylomic expression data
- epic.controls - ReadEPIC
- hannumCoef - Age Prediction from methylomic expression data
- iDMR - Imprinting differentially methylated region probes of Illumina 450 arrays
- melon - Small MethyLumi data set for examples and testing
- smokp_cpgs - Smoking Prediction from methylomic expression data
On BioConductor:wateRmelon-2.13.0(bioc 3.21)wateRmelon-2.12.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
dnamethylationmicroarraytwochannelpreprocessingqualitycontrol
Last updated 23 days agofrom:980e6cd313. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
Exports:adaptRefQuantilesadjustedDasenadjustedFunnormagepanSNPanti.trafoaogetas.methylumiauc_probabilitybeadcbeadcountBeta2MbetaqnbfpbgIntensitySwan.methylumiBMIQbsconbscon_methybscon_minficannoCheckBMIQcolnamescolumnMatrixcomboconcatenateMatricescoRankedMatricescorrectIcorrectIIdanendanesdanetdasendataDetectPval2NADataToNChannelSet2daten1daten2db1designIItoMandU2designItoMandU2detectionPval.filterdfortdfs2dfsfitdmrsedmrse_coldmrse_rowepicv2cleanepicv2clean.defaultepicv2clean.gds.classestimateCellCounts.wateRmelonestimateCellCounts.wmlnestimateSexextractAssayDataFromList2filterXYfindAnnotationProbesfotfuksgcomsgcosegenallgenerateManifestgenkigenkmegenkusgenmegenusgetControlProbes2getMethylationBeadMappers2getMethylumiBetagetQuantilesgetSamplesgetsnpgoodSNPgotIDATsToMatrices2IDATtoMatrix2idetiDMRiqrFunloadMethylumi2lumiMethyR2M2BetamergeProbeDesigns2methylumIDATepicmetricsmvFunnanesnanetnasennatennbBeadsFilterNChannelSetToMethyLumiSet2normalize.quantiles2normalizeIlluminaMethylationoutlyxoxyscalep_dfsfitpcoutedpfilterpipelineIlluminaMethylation.batchplot_predicted_sexpreprocessIlluminaMethylationpwodqualread.manifestreadEPICreadPeporeferenceQuantilesrobustQuantileNorm_Illumina450KrobustQuantileNorm_Illumina450K.probeCategoriesseabiseabi2seabirdseabird2sextestsmokpsort_ordersubbosummitsswantie_normtosttrafouniqueAnnotationCategoryuSexQNuSexQNengine
Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrevaluatefansifarverfastmapFDb.InfiniumMethylation.hg19foreachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableHDF5Arrayhighrhmshttrhttr2IlluminaHumanMethylation450kanno.ilmn12.hg19illuminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlatticelifecyclelimmalocfitlumimagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimulttestmunsellnleqslvnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrentrezreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsROCRsamtoolsRSQLitertracklayerrvestS4ArraysS4VectorsscalesscrimeselectrsiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Illumina 450K arrays: normalization and performance metrics | wateRmelon-package wateRmelon |
| Internal function to guess correct pData and retrieve using minfi | .createAnnotation |
| Internal functions for Illumina i450 normalization functions | .getManifestString fot got pop |
| Functions from 450-pipeline (Touleimat & Tost) | adaptRefQuantiles bgIntensitySwan.methylumi concatenateMatrices coRankedMatrices dataDetectPval2NA detectionPval.filter filterXY findAnnotationProbes getMethylumiBeta getQuantiles getSamples loadMethylumi2 lumiMethyR2 nbBeadsFilter normalize.quantiles2 normalizeIlluminaMethylation pipelineIlluminaMethylation.batch preprocessIlluminaMethylation referenceQuantiles robustQuantileNorm_Illumina450K robustQuantileNorm_Illumina450K.probeCategories uniqueAnnotationCategory |
| adjustedDasen | adjustedDasen |
| adjustedFunnorm | adjustedFunnorm |
| Age Prediction from methylomic expression data | agep agep,MethylSet-method agep,MethyLumiSet-method agep,RGChannelSet-method age_coefficients coef hannumCoef |
| Methods for Function 'as.methylumi' | as.methylumi as.methylumi,ANY-method as.methylumi,MethylSet-method as.methylumi,MethyLumiSet-method as.methylumi-methods getColumns |
| Calculates the number of samples with bead count <3 for each probe in matrix of bead count values | beadc |
| Creates matrix of beacounts from minfi data. | beadcount |
| Internal functions for peak.correction (fuks) | Beta2M correctI correctII M2Beta summits |
| Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays | betaqn,exprmethy450-method fuks,exprmethy450-method |
| Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays | BMIQ BMIQ,ANY-method BMIQ,MethylSet-method BMIQ,MethyLumiSet-method BMIQ-methods CheckBMIQ |
| Calculate bisulphite conversion | bscon bscon,MethyLumiSet-method bscon,RGChannelSet-method |
| canno - process csv manifest into annotation object for illumina methylation preprocessing | canno |
| Methods for Function 'colnames' in Package 'wateRmelon' | colnames,MethyLumiSet-method colnames-methods |
| Combine MethyLumiSet objects | combo |
| Calculate normalized betas from Illumina 450K methylation arrays | betaqn danen danes danet dasen daten1 daten2 fuks nanes nanet nasen naten swan tost |
| Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays | betaqn,MethyLumiSet-method danen,MethyLumiSet-method danes,MethyLumiSet-method danet,MethyLumiSet-method dasen,MethyLumiSet-method daten1,MethyLumiSet-method daten2,MethyLumiSet-method fuks,MethyLumiSet-method nanes,MethyLumiSet-method nanet,MethyLumiSet-method nasen,MethyLumiSet-method naten,MethyLumiSet-method swan,MethyLumiSet-method tost,MethyLumiSet-method |
| Calculate normalized betas from Illumina 450K methylation arrays | betaqn,MethylSet-method betaqn,RGChannelSet-method danen,MethylSet-method danen,RGChannelSet-method danes,MethylSet-method danes,RGChannelSet-method danet,MethylSet-method danet,RGChannelSet-method dasen,MethylSet-method dasen,RGChannelSet-method daten1,MethylSet-method daten1,RGChannelSet-method daten2,MethylSet-method daten2,RGChannelSet-method fuks,MethylSet-method fuks,RGChannelSet-method nanes,MethylSet-method nanes,RGChannelSet-method nanet,MethylSet-method nanet,RGChannelSet-method nasen,MethylSet-method nasen,RGChannelSet-method naten,MethylSet-method naten,RGChannelSet-method swan,MethylSet-method swan,RGChannelSet-method tost,MethylSet-method tost,RGChannelSet-method |
| Internal wateRmelon functions for calculating betas | db1 dfs2 dfsfit |
| Standard error of iDMR 450k array DNA methylation features | dmrse dmrse_col dmrse_row |
| Methods for Function 'dmrse' in Package 'wateRmelon' | dmrse,exprmethy450-method dmrse,MethylSet-method dmrse,MethyLumiSet-method dmrse,RGChannelSet-method dmrse-methods dmrse_col,exprmethy450-method dmrse_col,MethylSet-method dmrse_col,MethyLumiSet-method dmrse_col,RGChannelSet-method dmrse_col-methods dmrse_row,exprmethy450-method dmrse_row,MethylSet-method dmrse_row,MethyLumiSet-method dmrse_row,RGChannelSet-method dmrse_row-methods |
| Strip and subset EPICv2 data to work with legacy data and methods | epicv2clean epicv2clean.default epicv2clean.gds.class |
| Cell Proportion Estimation using wateRmelon | estimateCellCounts.wateRmelon estimateCellCounts.wateRmelon,MethylSet-method estimateCellCounts.wateRmelon,MethyLumiSet-method estimateCellCounts.wateRmelon,RGChannelSet-method estimateCellCounts.wmln |
| Predict sex by using robust sex-related CpG sites on ChrX and ChrY | estimateSex |
| SNP derived performance metrics for Illumina 450K DNA methylation arrays. | genki |
| Methods for Function 'genki' in Package 'wateRmelon' | genki,exprmethy450-method genki,MethylSet-method genki,MethyLumiSet-method genki,RGChannelSet-method genki-methods |
| Internal functions for genotype-based normalization metrics | gcoms gcose genkme genkus getsnp |
| Internal functions for Illumina i450 normalization functions | fot got |
| idet - identify idats by a hash of the addresses | idet |
| Imprinting differentially methylated region probes of Illumina 450 arrays | iDMR |
| Small MethyLumi data set for examples and testing | melon |
| Calculate a full set of 450K normalization/performance metrics | metrics |
| For internal use, is read using minfi-like machinery and then preprocessed into the more flexible and convenient methylumi object used by wateRmelon/bigmelon | NChannelSetToMethyLumiSet2 |
| Identify Outliers within Methylumi and Minfi packaged objects | outlyx |
| Methods for Function 'outlyx' in Package 'wateRmelon' | outlyx,MethylSet-method outlyx,MethyLumiSet-method outlyx,RGChannelSet-method |
| Basic data filtering for Illumina 450 methylation data | pfilter pfilter,MethyLumiSet-method pfilter,RGChannelSetExtended-method pfilter-methods |
| Probe-Wise Outlier Detection | pwod |
| Methods for Function 'pwod' in Package 'wateRmelon' | pwod,MethylSet-method pwod,MethyLumiSet-method pwod,RGChannelSet-method |
| A measure of Normalization Violence | qual |
| read.manifest - read in csv format Illumina chip manifest files | read.manifest |
| readEPIC | epic.controls readEPIC |
| readPepo - read (any kind of) Illumina DNA methylation array idat files into a methylumi object | readPepo |
| Calculate a performance metric based on male-female differences for Illumina methylation 450K arrays | seabi |
| Methods for Function 'seabi' in Package 'wateRmelon' | seabi,exprmethy450-method seabi,MethylSet-method seabi,MethyLumiSet-method seabi,RGChannelSet-method seabi-methods |
| Calculate ROC area-under-curve for X-chromosome sex differences (internal function for calculating the seabi metric) | seabird |
| Test Illumina methylation 450K array probes for sex difference (internal function for calculating 'seabi' performance metric) | sextest |
| Smoking Prediction from methylomic expression data | smokp smokp,MethylSet-method smokp,MethyLumiSet-method smokp,RGChannelSet-method smokp_cpgs |
| Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1 | anSNP anti.trafo aoget auc_probability bfp bscon_methy bscon_minfi columnMatrix DataToNChannelSet2 designIItoMandU2 designItoMandU2 dfort extractAssayDataFromList2 genall generateManifest genme genus getControlProbes2 getMethylationBeadMappers2 goodSNP IDATsToMatrices2 IDATtoMatrix2 iqrFun mergeProbeDesigns2 methylumIDATepic mvFun NChannelSetToMethyLumiSet2 oxyscale pcouted plot_predicted_sex p_dfsfit seabi2 seabird2 sort_order subbo tie_norm trafo uSexQN uSexQN,MethylSet-method uSexQN,MethyLumiSet-method uSexQN,RGChannelSet-method uSexQNengine |
