Package: wateRmelon 2.19.0

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:Leo C Schalkwyk [cre, aut], Tyler J Gorrie-Stone [aut], Ruth Pidsley [aut], Chloe CY Wong [aut], Nizar Touleimat [ctb], Matthieu Defrance [ctb], Andrew Teschendorff [ctb], Jovana Maksimovic [ctb], Louis Y El Khoury [ctb], Yucheng Wang [ctb], Alexandria Andrayas [ctb]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
wateRmelon/json (API)

# Install 'wateRmelon' in R:

install.packages('wateRmelon', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

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-2.19.0(bioc 3.24)wateRmelon-2.18.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dnamethylation microarray twochannel preprocessing qualitycontrol

7.81 score 6 packages 359 scripts 108 mentions 127 exports 166 dependencies

Last updated from:1bf46113db. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	616
linux-devel-x86_64	WARNING	939
source / vignettes	OK	750
linux-release-x86_64	WARNING	919
macos-release-arm64	WARNING	427
macos-oldrel-arm64	WARNING	602
windows-devel	WARNING	647
windows-release	WARNING	749
windows-oldrel	WARNING	706
wasm-release	OK	566

Exports:adaptRefQuantiles adjustedDasen adjustedFunnorm agep anSNP anti.trafo aoget as.methylumi auc_probability beadc beadcount Beta2M betaqn bfp bgIntensitySwan.methylumi BMIQ bscon bscon_methy bscon_minfi canno CheckBMIQ colnames columnMatrix combo concatenateMatrices coRankedMatrices correctI correctII danen danes danet dasen dataDetectPval2NA DataToNChannelSet2 daten1 daten2 db1 designIItoMandU2 designItoMandU2 detectionPval.filter detectP dfort dfs2 dfsfit dmrse dmrse_col dmrse_row epicv2clean epicv2clean.default epicv2clean.gds.class estimateCellCounts.wateRmelon estimateCellCounts.wmln estimateSex extractAssayDataFromList2 filterXY findAnnotationProbes fot fuks gcoms gcose genall generateManifest genki genkme genkus genme genus getControlProbes2 getMethylationBeadMappers2 getMethylumiBeta getQuantiles getSamples getsnp goodSNP got IDATsToMatrices2 IDATtoMatrix2 idet iDMR iqrFun loadMethylumi2 lumiMethyR2 M2Beta mergeProbeDesigns2 methylumIDATepic metrics mvFun nanes nanet nasen naten nbBeadsFilter NChannelSetToMethyLumiSet2 normalize.quantiles2 normalizeIlluminaMethylation outlyx oxyscale p_dfsfit pcouted pfilter pipelineIlluminaMethylation.batch plot_predicted_sex preprocessIlluminaMethylation pwod qual read.manifest readEPIC readPepo referenceQuantiles robustQuantileNorm_Illumina450K robustQuantileNorm_Illumina450K.probeCategories seabi seabi2 seabird seabird2 sextest smokp sort_order subbo summits swan tie_norm tost trafo uniqueAnnotationCategory uSexQN uSexQNengine

Dependencies:abind affy affyio annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocManager BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr evaluate farver fastmap FDb.InfiniumMethylation.hg19 filelock foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GEOquery ggplot2 glue gtable h5mread HDF5Array highr hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 illuminaio IRanges isoband iterators jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma locfit lumi magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise methylumi mgcv mime minfi multtest nleqslv nlme nor1mix openssl org.Hs.eg.db pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape reshape2 restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools ROC Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors S7 scales scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect TxDb.Hsapiens.UCSC.hg19.knownGene tzdb UCSC.utils utf8 vctrs viridisLite vroom withr xfun XML xml2 xtable XVector yaml

The wateRmelon User's Guide

Rendered fromwateRmelon.Rmdusingknitr::rmarkdown

Last update: 2023-09-05
Started: 2023-09-04

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

Package: wateRmelon 2.19.0

wateRmelon: Illumina DNA methylation array normalization and metrics

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