# Illumina DNA methylation array normalization and metrics

## Documentation for package ‘wateRmelon’ version 2.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I L M N O P Q R S T U W misc

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

## -- A --

adaptRefQuantiles | Functions from 450-pipeline (Touleimat & Tost)
adjustedDasen | adjustedDasen
adjustedFunnorm | adjustedFunnorm
agep | Age Prediction from methylomic expression data
agep-method | Age Prediction from methylomic expression data
age_coefficients | Age Prediction from methylomic expression data
anSNP | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
anti.trafo | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
aoget | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
as.methylumi | Methods for Function 'as.methylumi'
as.methylumi-method | Methods for Function 'as.methylumi'
as.methylumi-methods | Methods for Function 'as.methylumi'
auc_probability | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- B --

beadc | Calculates the number of samples with bead count <3 for each probe in matrix of bead count values
beadcount | Creates matrix of beacounts from minfi data.
Beta2M | Internal functions for peak.correction (fuks)
betaqn | Calculate normalized betas from Illumina 450K methylation arrays
betaqn-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
betaqn-method | Calculate normalized betas from Illumina 450K methylation arrays
betaqn-method | Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays
bfp | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
bgIntensitySwan.methylumi | Functions from 450-pipeline (Touleimat & Tost)
BMIQ | Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays
BMIQ-method | Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays
BMIQ-methods | Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays
bscon | Calculate bisulphite conversion
bscon-method | Calculate bisulphite conversion
bscon_methy | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
bscon_minfi | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- C --

canno | canno - process csv manifest into annotation object for illumina methylation preprocessing
CheckBMIQ | Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays
coef | Age Prediction from methylomic expression data
colnames-method | Methods for Function 'colnames' in Package 'wateRmelon'
colnames-methods | Methods for Function 'colnames' in Package 'wateRmelon'
columnMatrix | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
combo | Combine MethyLumiSet objects
concatenateMatrices | Functions from 450-pipeline (Touleimat & Tost)
coRankedMatrices | Functions from 450-pipeline (Touleimat & Tost)
correctI | Internal functions for peak.correction (fuks)
correctII | Internal functions for peak.correction (fuks)

## -- D --

danen | Calculate normalized betas from Illumina 450K methylation arrays
danen-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
danen-method | Calculate normalized betas from Illumina 450K methylation arrays
danes | Calculate normalized betas from Illumina 450K methylation arrays
danes-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
danes-method | Calculate normalized betas from Illumina 450K methylation arrays
danet | Calculate normalized betas from Illumina 450K methylation arrays
danet-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
danet-method | Calculate normalized betas from Illumina 450K methylation arrays
dasen | Calculate normalized betas from Illumina 450K methylation arrays
dasen-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
dasen-method | Calculate normalized betas from Illumina 450K methylation arrays
dataDetectPval2NA | Functions from 450-pipeline (Touleimat & Tost)
DataToNChannelSet2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
daten1 | Calculate normalized betas from Illumina 450K methylation arrays
daten1-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
daten1-method | Calculate normalized betas from Illumina 450K methylation arrays
daten2 | Calculate normalized betas from Illumina 450K methylation arrays
daten2-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
daten2-method | Calculate normalized betas from Illumina 450K methylation arrays
db1 | Internal wateRmelon functions for calculating betas
designIItoMandU2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
designItoMandU2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
detectionPval.filter | Functions from 450-pipeline (Touleimat & Tost)
dfort | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
dfs2 | Internal wateRmelon functions for calculating betas
dfsfit | Internal wateRmelon functions for calculating betas
dmrse | Standard error of iDMR 450k array DNA methylation features
dmrse-method | Methods for Function 'dmrse' in Package 'wateRmelon'
dmrse-methods | Methods for Function 'dmrse' in Package 'wateRmelon'
dmrse_col | Standard error of iDMR 450k array DNA methylation features
dmrse_col-method | Methods for Function 'dmrse' in Package 'wateRmelon'
dmrse_col-methods | Methods for Function 'dmrse' in Package 'wateRmelon'
dmrse_row | Standard error of iDMR 450k array DNA methylation features
dmrse_row-method | Methods for Function 'dmrse' in Package 'wateRmelon'
dmrse_row-methods | Methods for Function 'dmrse' in Package 'wateRmelon'

## -- E --

epic.controls | readEPIC
epicv2clean | Strip and subset EPICv2 data to work with legacy data and methods
epicv2clean.default | Strip and subset EPICv2 data to work with legacy data and methods
epicv2clean.gds.class | Strip and subset EPICv2 data to work with legacy data and methods
estimateCellCounts.wateRmelon | Cell Proportion Estimation using wateRmelon
estimateCellCounts.wateRmelon-method | Cell Proportion Estimation using wateRmelon
estimateCellCounts.wmln | Cell Proportion Estimation using wateRmelon
estimateSex | Predict sex by using robust sex-related CpG sites on ChrX and ChrY
extractAssayDataFromList2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- F --

filterXY | Functions from 450-pipeline (Touleimat & Tost)
findAnnotationProbes | Functions from 450-pipeline (Touleimat & Tost)
fot | Internal functions for Illumina i450 normalization functions
fot | Internal functions for Illumina i450 normalization functions
fuks | Calculate normalized betas from Illumina 450K methylation arrays
fuks-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
fuks-method | Calculate normalized betas from Illumina 450K methylation arrays
fuks-method | Calculate normalized betas from exprmethy450 of Illumina 450K methylation arrays

## -- G --

gcoms | Internal functions for genotype-based normalization metrics
gcose | Internal functions for genotype-based normalization metrics
genall | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
generateManifest | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
genki | SNP derived performance metrics for Illumina 450K DNA methylation arrays.
genki-method | Methods for Function 'genki' in Package 'wateRmelon'
genki-methods | Methods for Function 'genki' in Package 'wateRmelon'
genkme | Internal functions for genotype-based normalization metrics
genkus | Internal functions for genotype-based normalization metrics
genme | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
genus | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
getColumns | Methods for Function 'as.methylumi'
getControlProbes2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
getMethylationBeadMappers2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
getMethylumiBeta | Functions from 450-pipeline (Touleimat & Tost)
getQuantiles | Functions from 450-pipeline (Touleimat & Tost)
getSamples | Functions from 450-pipeline (Touleimat & Tost)
getsnp | Internal functions for genotype-based normalization metrics
goodSNP | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
got | Internal functions for Illumina i450 normalization functions
got | Internal functions for Illumina i450 normalization functions

## -- H --

hannumCoef | Age Prediction from methylomic expression data

## -- I --

IDATsToMatrices2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
IDATtoMatrix2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
idet | idet - identify idats by a hash of the addresses
iDMR | Imprinting differentially methylated region probes of Illumina 450 arrays
iqrFun | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- L --

loadMethylumi2 | Functions from 450-pipeline (Touleimat & Tost)
lumiMethyR2 | Functions from 450-pipeline (Touleimat & Tost)

## -- M --

M2Beta | Internal functions for peak.correction (fuks)
melon | Small MethyLumi data set for examples and testing
mergeProbeDesigns2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
methylumIDATepic | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
metrics | Calculate a full set of 450K normalization/performance metrics
mvFun | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- N --

nanes | Calculate normalized betas from Illumina 450K methylation arrays
nanes-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
nanes-method | Calculate normalized betas from Illumina 450K methylation arrays
nanet | Calculate normalized betas from Illumina 450K methylation arrays
nanet-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
nanet-method | Calculate normalized betas from Illumina 450K methylation arrays
nasen | Calculate normalized betas from Illumina 450K methylation arrays
nasen-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
nasen-method | Calculate normalized betas from Illumina 450K methylation arrays
naten | Calculate normalized betas from Illumina 450K methylation arrays
naten-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
naten-method | Calculate normalized betas from Illumina 450K methylation arrays
nbBeadsFilter | Functions from 450-pipeline (Touleimat & Tost)
NChannelSetToMethyLumiSet2 | 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 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
normalize.quantiles2 | Functions from 450-pipeline (Touleimat & Tost)
normalizeIlluminaMethylation | Functions from 450-pipeline (Touleimat & Tost)

## -- O --

outlyx | Identify Outliers within Methylumi and Minfi packaged objects
outlyx-method | Methods for Function 'outlyx' in Package 'wateRmelon'
oxyscale | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- P --

pcouted | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
pfilter | Basic data filtering for Illumina 450 methylation data
pfilter-method | Basic data filtering for Illumina 450 methylation data
pfilter-methods | Basic data filtering for Illumina 450 methylation data
pipelineIlluminaMethylation.batch | Functions from 450-pipeline (Touleimat & Tost)
plot_predicted_sex | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
pop | Internal functions for Illumina i450 normalization functions
preprocessIlluminaMethylation | Functions from 450-pipeline (Touleimat & Tost)
pwod | Probe-Wise Outlier Detection
pwod-method | Methods for Function 'pwod' in Package 'wateRmelon'
p_dfsfit | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- Q --

qual | A measure of Normalization Violence

## -- R --

read.manifest | read.manifest - read in csv format Illumina chip manifest files
readEPIC | readEPIC
readPepo | readPepo - read (any kind of) Illumina DNA methylation array idat files into a methylumi object
referenceQuantiles | Functions from 450-pipeline (Touleimat & Tost)
robustQuantileNorm_Illumina450K | Functions from 450-pipeline (Touleimat & Tost)
robustQuantileNorm_Illumina450K.probeCategories | Functions from 450-pipeline (Touleimat & Tost)

## -- S --

seabi | Calculate a performance metric based on male-female differences for Illumina methylation 450K arrays
seabi-method | Methods for Function 'seabi' in Package 'wateRmelon'
seabi-methods | Methods for Function 'seabi' in Package 'wateRmelon'
seabi2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
seabird | Calculate ROC area-under-curve for X-chromosome sex differences (internal function for calculating the seabi metric)
seabird2 | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
sextest | Test Illumina methylation 450K array probes for sex difference (internal function for calculating 'seabi' performance metric)
smokp | Smoking Prediction from methylomic expression data
smokp-method | Smoking Prediction from methylomic expression data
smokp_cpgs | Smoking Prediction from methylomic expression data
sort_order | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
subbo | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
summits | Internal functions for peak.correction (fuks)
swan | Calculate normalized betas from Illumina 450K methylation arrays
swan-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
swan-method | Calculate normalized betas from Illumina 450K methylation arrays

## -- T --

tie_norm | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
tost | Calculate normalized betas from Illumina 450K methylation arrays
tost-method | Calculate normalized betas from MethyLumiSets of Illumina 450K methylation arrays
tost-method | Calculate normalized betas from Illumina 450K methylation arrays
trafo | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- U --

uniqueAnnotationCategory | Functions from 450-pipeline (Touleimat & Tost)
uSexQN | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
uSexQN-method | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1
uSexQNengine | Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

## -- W --

wateRmelon | Illumina 450K arrays: normalization and performance metrics

## -- misc --

.createAnnotation | Internal function to guess correct pData and retrieve using minfi
.getManifestString | Internal functions for Illumina i450 normalization functions