wateRmelon: Illumina 450 methylation array normalization and metrics

15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.

AuthorLeonard C Schalkwyk, Ruth Pidsley, Chloe CY Wong, with functions contributed by Nizar Touleimat, Matthieu Defrance, Andrew Teschendorff, Jovana Maksimovic, Tyler Gorrie-Stone, Louis El Khoury
Date of publicationNone
MaintainerLeo <lschal@essex.ac.uk>
LicenseGPL-3
Version1.18.0

View on Bioconductor

Man pages

adaptRefQuantiles: Functions from 450-pipeline (Touleimat & Tost)

agep: Age Prediction from methylomic expression data

as.methylumi-methods: Methods for Function 'as.methylumi'

beadc: Calculates the number of samples with bead count <3 for each...

beadcount: Creates matrix of beacounts from minfi data.

Beta2M: Internal functions for peak.correction (fuks)

BMIQ: Beta-Mixture Quantile (BMIQ) Normalisation method for...

bscon: Calculate bisulphite conversion

colnames-methods: Methods for Function 'colnames' in Package 'wateRmelon'

combo: Combine MethyLumiSet objects

dasen: Calculate normalized betas from Illumina 450K methylation...

dasen-exprmethy450: Calculate normalized betas from exprmethy450 of Illumina 450K...

dasen-MethyLumiSet: Calculate normalized betas from MethyLumiSets of Illumina...

dasen-MethySet: Calculate normalized betas from Illumina 450K methylation...

db1: Internal wateRmelon functions for calculating betas

dmrse: Standard error of iDMR 450k array DNA methylation features

dmrse-methods: Methods for Function 'dmrse' in Package 'wateRmelon'

genki: SNP derived performance metrics for Illumina 450K DNA...

genki-methods: Methods for Function 'genki' in Package 'wateRmelon'

genkme: Internal functions for genotype-based normalization metrics

got: Internal functions for Illumina i450 normalization functions

iDMR: Imprinting differentially methylated region probes of...

melon: Small MethyLumi data set for examples and testing

metrics: Calculate a full set of 450K normalization/performance...

outlyx: Identify Outliers within Methylumi and Minfi packaged objects

outlyx-methods: Methods for Function 'outlyx' in Package 'wateRmelon'

pfilter: Basic data filtering for Illumina 450 methylation data

pwod: Probe-Wise Outlier Detection

pwod-methods: Methods for Function 'pwod' in Package 'wateRmelon'

qual: A measure of Normalization Violence

readEPIC: readEPIC

seabi: Calculate a performance metric based on male-female...

seabi-methods: Methods for Function 'seabi' in Package 'wateRmelon'

seabird: Calculate ROC area-under-curve for X-chromosome sex...

sextest: Test Illumina methylation 450K array probes for sex...

wateRmelon-package: Illumina 450K arrays: normalization and performance metrics

wm_internal: Internal functions for readEPIC and other wateRmelon...

Files in this package

wateRmelon/DESCRIPTION
wateRmelon/NAMESPACE
wateRmelon/NEWS
wateRmelon/R
wateRmelon/R/AllGenerics.R wateRmelon/R/BMIQ_1.1.R wateRmelon/R/Beta2M.R wateRmelon/R/M2Beta.R wateRmelon/R/adaptRefQuantiles.R wateRmelon/R/as.methylumi.R wateRmelon/R/beta1.R wateRmelon/R/betaqn.R wateRmelon/R/bgeq.R wateRmelon/R/bgeqot.R wateRmelon/R/bgeqq2.R wateRmelon/R/bgeqqn.R wateRmelon/R/bscon.R wateRmelon/R/bscon_methy.R wateRmelon/R/bscon_minfi.R wateRmelon/R/coRankedMatrices.R wateRmelon/R/combo.R wateRmelon/R/concatenateMatrices.R wateRmelon/R/correctI.R wateRmelon/R/correctII.R wateRmelon/R/dataDetectPval2NA.R wateRmelon/R/db1.R wateRmelon/R/detectionPval.filter.R wateRmelon/R/dfs2.R wateRmelon/R/dfsfit.R wateRmelon/R/dmrse.R wateRmelon/R/dmrse_col.R wateRmelon/R/dmrse_row.R wateRmelon/R/dyebuy1.R wateRmelon/R/dyebuy2.R wateRmelon/R/dyebuy3.R wateRmelon/R/dyebuy4.R wateRmelon/R/filterXY.R wateRmelon/R/findAnnotationProbes.R wateRmelon/R/gcoms.R wateRmelon/R/gcose.R wateRmelon/R/genki.R wateRmelon/R/genkme.R wateRmelon/R/genkus.R wateRmelon/R/genotype.R wateRmelon/R/getAnn.R wateRmelon/R/getMethylumiBeta.R wateRmelon/R/getQuantiles.R wateRmelon/R/getSamples.R wateRmelon/R/getsnp.R wateRmelon/R/horv.R wateRmelon/R/loadMethylumi2.R wateRmelon/R/lumiMethyR2.R wateRmelon/R/melon.R wateRmelon/R/nbBeadsFilter.R wateRmelon/R/normalize.quantiles2.R wateRmelon/R/normalizeIlluminaMethylation.R wateRmelon/R/ot.R wateRmelon/R/outlyx.R wateRmelon/R/oxyscale.R wateRmelon/R/pasteque.R wateRmelon/R/peak.correction.R wateRmelon/R/pfilter.R wateRmelon/R/pipelineIlluminaMethylation.batch.R wateRmelon/R/preprocessIlluminaMethylation.R wateRmelon/R/pwod.R wateRmelon/R/qual.R wateRmelon/R/readEPIC.R wateRmelon/R/referenceQuantiles.R wateRmelon/R/robustQuantileNorm_Illumina450K.R wateRmelon/R/robustQuantileNorm_Illumina450K.probeCategories.R wateRmelon/R/seabird.R wateRmelon/R/sextest.R wateRmelon/R/summits.R wateRmelon/R/swan2.R wateRmelon/R/uniqueAnnotationCategory.R wateRmelon/R/x_methylumi.R wateRmelon/R/y_minfi.R
wateRmelon/build
wateRmelon/build/vignette.rds
wateRmelon/data
wateRmelon/data/coef.rda
wateRmelon/data/datalist
wateRmelon/data/epic.controls.rda
wateRmelon/data/epic.ordering.rda
wateRmelon/data/iDMR.rda
wateRmelon/data/melon.rda
wateRmelon/inst
wateRmelon/inst/CITATION
wateRmelon/inst/doc
wateRmelon/inst/doc/wateRmelon.R
wateRmelon/inst/doc/wateRmelon.Rnw
wateRmelon/inst/doc/wateRmelon.pdf
wateRmelon/man
wateRmelon/man/BMIQ.Rd wateRmelon/man/Beta2M.Rd wateRmelon/man/adaptRefQuantiles.Rd wateRmelon/man/agep.Rd wateRmelon/man/as.methylumi-methods.Rd wateRmelon/man/beadc.Rd wateRmelon/man/beadcount.Rd wateRmelon/man/bscon.Rd wateRmelon/man/colnames-methods.Rd wateRmelon/man/combo.Rd wateRmelon/man/dasen-MethyLumiSet.Rd wateRmelon/man/dasen-MethySet.Rd wateRmelon/man/dasen-exprmethy450.Rd wateRmelon/man/dasen.Rd wateRmelon/man/db1.Rd wateRmelon/man/dmrse-methods.Rd wateRmelon/man/dmrse.Rd wateRmelon/man/genki-methods.Rd wateRmelon/man/genki.Rd wateRmelon/man/genkme.Rd wateRmelon/man/got.Rd wateRmelon/man/iDMR.Rd wateRmelon/man/melon.Rd wateRmelon/man/metrics.Rd wateRmelon/man/outlyx-methods.Rd wateRmelon/man/outlyx.Rd wateRmelon/man/pfilter.Rd wateRmelon/man/pwod-methods.Rd wateRmelon/man/pwod.Rd wateRmelon/man/qual.Rd wateRmelon/man/readEPIC.Rd wateRmelon/man/seabi-methods.Rd wateRmelon/man/seabi.Rd wateRmelon/man/seabird.Rd wateRmelon/man/sextest.Rd wateRmelon/man/wateRmelon-package.Rd wateRmelon/man/wm_internal.Rd
wateRmelon/vignettes
wateRmelon/vignettes/wateRmelon.Rnw

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