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.

Author
Leonard 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 publication
None
Maintainer
Leo <lschal@essex.ac.uk>
License
GPL-3
Version
1.18.0

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