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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("wateRmelon")
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
Bioconductor views DNAMethylation Microarray Preprocessing QualityControl TwoChannel
Date of publicationNone
MaintainerLeo <lschal@essex.ac.uk>
LicenseGPL-3
Version1.20.0

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...

Functions

adaptRefQuantiles Man page
agep Man page
agep,MethylSet-method Man page
agep,MethyLumiSet-method Man page
anSNP Man page
anti.trafo Man page
aoget Man page
as.methylumi Man page
as.methylumi,ANY-method Man page
as.methylumi-methods Man page
as.methylumi,MethylSet-method Man page
as.methylumi,MethyLumiSet-method Man page
beadc Man page
beadcount Man page
Beta2M Man page
betaqn Man page
betaqn,exprmethy450-method Man page
betaqn,MethylSet-method Man page
betaqn,MethyLumiSet-method Man page
betaqn,RGChannelSet-method Man page
bfp Man page
bgIntensitySwan.methylumi Man page
BMIQ Man page
BMIQ,ANY-method Man page
BMIQ-methods Man page
BMIQ,MethylSet-method Man page
BMIQ,MethyLumiSet-method Man page
bscon Man page
bscon_methy Man page
bscon,MethyLumiSet-method Man page
bscon_minfi Man page
bscon,RGChannelSet-method Man page
CheckBMIQ Man page
coef Man page
colnames-methods Man page
colnames,MethyLumiSet-method Man page
columnMatrix Man page
combo Man page
concatenateMatrices Man page
coRankedMatrices Man page
correctI Man page
correctII Man page
danen Man page
danen,MethylSet-method Man page
danen,MethyLumiSet-method Man page
danen,RGChannelSet-method Man page
danes Man page
danes,MethylSet-method Man page
danes,MethyLumiSet-method Man page
danes,RGChannelSet-method Man page
danet Man page
danet,MethylSet-method Man page
danet,MethyLumiSet-method Man page
danet,RGChannelSet-method Man page
dasen Man page
dasen,MethylSet-method Man page
dasen,MethyLumiSet-method Man page
dasen,RGChannelSet-method Man page
dataDetectPval2NA Man page
DataToNChannelSet2 Man page
daten1 Man page
daten1,MethylSet-method Man page
daten1,MethyLumiSet-method Man page
daten1,RGChannelSet-method Man page
daten2 Man page
daten2,MethylSet-method Man page
daten2,MethyLumiSet-method Man page
daten2,RGChannelSet-method Man page
db1 Man page
designIItoMandU2 Man page
designItoMandU2 Man page
detectionPval.filter Man page
dfort Man page
dfs2 Man page
dfsfit Man page
dmrse Man page
dmrse_col Man page
dmrse_col,exprmethy450-method Man page
dmrse_col-methods Man page
dmrse_col,MethylSet-method Man page
dmrse_col,MethyLumiSet-method Man page
dmrse_col,RGChannelSet-method Man page
dmrse,exprmethy450-method Man page
dmrse-methods Man page
dmrse,MethylSet-method Man page
dmrse,MethyLumiSet-method Man page
dmrse,RGChannelSet-method Man page
dmrse_row Man page
dmrse_row,exprmethy450-method Man page
dmrse_row-methods Man page
dmrse_row,MethylSet-method Man page
dmrse_row,MethyLumiSet-method Man page
dmrse_row,RGChannelSet-method Man page
epic.controls Man page
epic.ordering Man page
extractAssayDataFromList2 Man page
filterXY Man page
findAnnotationProbes Man page
fot Man page
fuks Man page
fuks,exprmethy450-method Man page
fuks,MethylSet-method Man page
fuks,MethyLumiSet-method Man page
fuks,RGChannelSet-method Man page
gcoms Man page
gcose Man page
genall Man page
genki Man page
genki,exprmethy450-method Man page
genki-methods Man page
genki,MethylSet-method Man page
genki,MethyLumiSet-method Man page
genki,RGChannelSet-method Man page
genkme Man page
genkus Man page
genme Man page
genus Man page
getColumns Man page
getControlProbes2 Man page
getMethylationBeadMappers2 Man page
getMethylumiBeta Man page
getQuantiles Man page
getSamples Man page
getsnp Man page
goodSNP Man page
got Man page
IDATsToMatrices2 Man page
IDATtoMatrix2 Man page
iDMR Man page
iqrFun Man page
loadMethylumi2 Man page
lumiMethyR2 Man page
M2Beta Man page
melon Man page
mergeProbeDesigns2 Man page
methylumIDATepic Man page
metrics Man page
mvFun Man page
nanes Man page
nanes,MethylSet-method Man page
nanes,MethyLumiSet-method Man page
nanes,RGChannelSet-method Man page
nanet Man page
nanet,MethylSet-method Man page
nanet,MethyLumiSet-method Man page
nanet,RGChannelSet-method Man page
nasen Man page
nasen,MethylSet-method Man page
nasen,MethyLumiSet-method Man page
nasen,RGChannelSet-method Man page
naten Man page
naten,MethylSet-method Man page
naten,MethyLumiSet-method Man page
naten,RGChannelSet-method Man page
nbBeadsFilter Man page
NChannelSetToMethyLumiSet2 Man page
normalizeIlluminaMethylation Man page
normalize.quantiles2 Man page
outlyx Man page
outlyx,MethylSet-method Man page
outlyx,MethyLumiSet-method Man page
outlyx,RGChannelSet-method Man page
oxyscale Man page
pcouted Man page
pfilter Man page
pfilter-methods Man page
pfilter,MethyLumiSet-method Man page
pfilter,RGChannelSetExtended-method Man page
pipelineIlluminaMethylation.batch Man page
pop Man page
preprocessIlluminaMethylation Man page
pwod Man page
pwod,MethylSet-method Man page
pwod,MethyLumiSet-method Man page
pwod,RGChannelSet-method Man page
qual Man page
readEPIC Man page
referenceQuantiles Man page
robustQuantileNorm_Illumina450K Man page
robustQuantileNorm_Illumina450K.probeCategories Man page
seabi Man page
seabi,exprmethy450-method Man page
seabi-methods Man page
seabi,MethylSet-method Man page
seabi,MethyLumiSet-method Man page
seabird Man page
seabi,RGChannelSet-method Man page
sextest Man page
summits Man page
swan Man page
swan,MethylSet-method Man page
swan,MethyLumiSet-method Man page
swan,RGChannelSet-method Man page
tost Man page
tost,MethylSet-method Man page
tost,MethyLumiSet-method Man page
tost,RGChannelSet-method Man page
trafo Man page
uniqueAnnotationCategory Man page
wateRmelon Man page
wateRmelon-package Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.