Package ‘wateRmelon’ - Bioconductor - Home

1 Package watermelon September 29, 2020 TypePackageTitleIllumina 450 methylation array normalization and C Schalkwyk, Ruth Pidsley, Chloe CY Wong, with functions con-tributed by Nizar Touleimat, Matthieu Defrance, Andrew Teschendorff, Jovana Maksi-movic, Tyler Gorrie-Stone, Louis El flavours of betas and three performance metrics, with methods for objects pro-duced by methylumi and minfi (>= ), Biobase, limma, methods, matrixStats, methylumi,lumi, ROC, ,illuminaioImportsBiobaseEnhancesminfiSu ggestsRPMM, ,IlluminaHumanMethylationEPIC manifest, irlbaLazyLoadyesbiocViewsDNAM ethylation, Microarray, TwoChannel, Preprocessing, documented: watermelon - Package .

2 3adaptRefQuantiles ..3agep ..5beadc ..6beadcount ..6 Beta2M ..7betaqn-exprmethy450-methods ..8 BMIQ ..9bscon .. 11colnames-methods .. 12combo .. 12dasen .. 13dasen-methods .. 15dasen-minfi-methods .. 17db1 .. 18dmrse .. 20dmrse-methods .. 21estimateCellCounts .. 21genki .. 23genki-methods .. 24genkme .. 24got .. 25iDMR .. 26melon .. 26metrics .. 27outlyx .. 28outlyx-methods .. 29pfilter .. 29predictSex .. 31pwod .. 32pwod-methods .. 32qual .. 33readEPIC .. 33seabi .. 35seabi-methods.

3 36seabird .. 36sextest .. 37wm_internal .. 38adaptRefQuantiles3 Index39wateRmelon-packageIllumina 450K arrays: normalization and performance metricsDescriptionFunctions for calculating the index of DNA methylation proportion beta in 15 different ways, andthree different ways of estimating data quality or normalization :wateRmelonType: :2012-10-10 License:GPL3 Author(s)Leonard C Schalkwyk, Ruth Pidsley and Chloe Wong Maintainer: Who to complain to R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach topreprocessing Illumina 450K methylation array data (submitted)adaptRefQuantilesFunctions from 450-pipeline (Touleimat & Tost)DescriptionThese functions are part of the 450K pipeline (Touleimat and Tost, Epigenomics 2012 4:325).

4 Forfreestanding use of the normalization function, a wrapper is provided, seetostAuthor(s)Nizar Touleimat, wrapper by N, Tost J: Complete pipeline for Infinium R Human Methylation 450K BeadChip dataprocessing using subset quantile normalization for accurate DNA methylation estimation. Epige-nomics 2012, 4:325-341 Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach topreprocessing Illumina 450K methylation array data (submitted)4agepagepAge Prediction from methylomic expression dataDescriptionPredict age of samples using Horvaths CoefficientsUsageagep(betas, coeff=NULL, method=c('horvath','hannum').)

5 ArgumentsbetasMatrix of betas or MethyLumiSet or MethylSet NULL, will default to Horvaths coefficients. Otherwise can be supplied withvector of own coefficients with an intercept as first either "horvath" or "hannum". If using "hannum" remember to calldata(hannumCoef) before analysis and supply coeff with the hannum coeffi-cients, otherwise will default to "horvath"..To pass to arguments to downstream functions to specify matrix of predicted ages per (s)Original Functions: Steve HorvathwateRmelon Implementation: Leo Schalkwyk, Louis El KhouryReferencesHorvath S: DNA methylation age of human tissues and cell types.

6 Genome Biology 2013, 14:R115 Examplesdata(melon)data(coef)agep(melon, coeff=coef)# oragep(betas(melon),coeff=coef) for a MethyLumiSet object populaed with the data provided. There are MethyLumiSet andMethylSet methods. In the default method, the data is all optional. Please note that for the resultsto be sane, mn, un, bn, and pv have to be in the same sample and feature order and the same function does not currently do any checks!Usage# default (mn = NULL, un = NULL, bn = NULL, pv = NULL, qc = NULL, da = NULL,..)Argumentsmnmatrix of methylated signal intensities, each column representing a sample (generic)or a MethyLumiSet, RGSet, or MethylSet object.

7 Column names are used to getSentrix row and column by default, see ..unmatrix of unmethylated signal intensities, each column representing a sample(default method) or NULL when mn is an object containing methylated andunmethylated valuesbnmatrix of precalculated betas, each column representing a samplepvmatrix of detection p-values, each column representing a sampledaannotation data frame, such as x@featureData@data #methylumi Package . IfNULL (the default), theIlluminaHumanMethylation450kmanifestp ackageis used. See the fd argumentqccontrol probe intensities: list of 2 matrices, Cy3 and Cy5, with rownames, suchas produced by intensitiesByChannel(QCdata(x)) (methylumi Package ).

8 Other arguments such as a featureData object or optional assayDataMethodssignature(mn = "MethylSet")Coerces a MethylSet to a MethyLumiSet, and provides it with aset of featureData, which by default is just the chromosome and DESIGN (ie typeI or typeII assay). Other data can be included using thefdargument, available data is listed by thefunctiongetColumns()signature(mn = "MethyLumiSet")This is mainly useful for adding featureData as described un-der MethylSet above. MethyLumiSet objects produced by methylumiR have the full annota-tion, those from methylumIDAT do not, and functions such asswanrequire itsignature(mn = "ANY") (mn = NULL,un = NULL,bn = NULL,pv = NULL,qc = NULL,da= NULL,fd = c("CHR","DESIGN"))6beadcountbeadcCalcula tes the number of samples with bead count <3 for each probein matrix of bead count valuesDescriptionCalculates the number of samples with bead count <3 for each probe in matrix of bead count (x)

9 Argumentsxmatrix of bead count values returned by the beadcount functionValueVector of number of samples with bead count <3 for each probeNoteThe beadc function is internal to the pfilter Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC: A data-driven approach topreprocessing Illumina 450K methylation array data (submitted)beadcountCreates matrix of beacounts from minfi matrix of beacounts from data read in using the minfi Package . NAs represent probes withbeadcount <3. An Extended RG Channel Set is required for this function to (x)Argumentsx450K methylation data read in using minfi to create an Extended RG ChannelSetBeta2M7 ValueA matrix of bead counts with bead counts <3 represented by NA for use in the pfilter function forquality controlNoteThe beadcount function is internal to the pfilter Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC.

10 A data-driven approach topreprocessing Illumina 450K methylation array data (submitted)Beta2 MInternal functions for (fuks)DescriptionInternal functions for (B)ArgumentsBa vector or matrix of beta values for conversionValuea vector or matrix of the same shape as the inputAuthor(s)Matthieu Defrance S, Defrance M, Calonne E, Sotiriou C, Fuks F: Evaluation of the Infinium Methy-lation 450K technology . Epigenetics 2011, 3(6) normalized betas from exprmethy450 of Illumina 450 Kmethylation arraysDescriptionQuantile normalize betas from exprmethy450 objectsArgumentsbnAn exprmethy450 added to total intensity to prevent denominators close to zero when calcu-lating betasDetailsbetaqnquantile normalizes betasValueexprmethy450 object of the same shape and order as Pidsley R, Wong CCY, Volta M, Lunnon K, Mill J, Schalkwyk LC.