.createAnnotation       Internal function to guess correct pData and
                        retrieve using minfi
.getManifestString      Internal functions for Illumina i450
                        normalization functions
BMIQ                    Beta-Mixture Quantile (BMIQ) Normalisation
                        method for Illumina 450k arrays
Beta2M                  Internal functions for peak.correction (fuks)
DataToNChannelSet2      Internal functions for readEPIC and other
                        wateRmelon functions introduced in v 1.13.1
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
adaptRefQuantiles       Functions from 450-pipeline (Touleimat & Tost)
adjustedDasen           adjustedDasen
adjustedFunnorm         adjustedFunnorm
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 probe in matrix of bead count
                        values
beadcount               Creates matrix of beacounts from minfi data.
betaqn,exprmethy450-method
                        Calculate normalized betas from exprmethy450 of
                        Illumina 450K methylation arrays
bscon                   Calculate bisulphite conversion
canno                   canno - process csv manifest into annotation
                        object for illumina methylation preprocessing
colnames-methods        Methods for Function 'colnames' in Package
                        'wateRmelon'
combo                   Combine MethyLumiSet objects
dasen                   Calculate normalized betas from Illumina 450K
                        methylation arrays
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'
epicv2clean.default     Strip and subset EPICv2 data to work with
                        legacy data and methods
estimateCellCounts.wmln
                        Cell Proportion Estimation using wateRmelon
estimateSex             Predict sex by using robust sex-related CpG
                        sites on ChrX and ChrY
genki                   SNP derived performance metrics for Illumina
                        450K DNA methylation arrays.
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 Illumina 450 arrays
idet                    idet - identify idats by a hash of the
                        addresses
melon                   Small MethyLumi data set for examples and
                        testing
metrics                 Calculate a full set of 450K
                        normalization/performance metrics
naten,MethyLumiSet-method
                        Calculate normalized betas from MethyLumiSets
                        of Illumina 450K methylation arrays
naten,MethylSet-method
                        Calculate normalized betas from Illumina 450K
                        methylation arrays
outlyx                  Identify Outliers within Methylumi and Minfi
                        packaged objects
outlyx,MethylSet-method
                        Methods for Function 'outlyx' in Package
                        'wateRmelon'
pfilter                 Basic data filtering for Illumina 450
                        methylation data
pwod                    Probe-Wise Outlier Detection
pwod,MethylSet-method   Methods for Function 'pwod' in Package
                        'wateRmelon'
qual                    A measure of Normalization Violence
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
seabi                   Calculate a performance metric based on
                        male-female differences for Illumina
                        methylation 450K arrays
seabi-methods           Methods for Function 'seabi' in Package
                        'wateRmelon'
seabird                 Calculate ROC area-under-curve for X-chromosome
                        sex differences (internal function for
                        calculating the seabi metric)
sextest                 Test Illumina methylation 450K array probes for
                        sex difference (internal function for
                        calculating 'seabi' performance metric)
smokp                   Smoking Prediction from methylomic expression
                        data
wateRmelon-package      Illumina 450K arrays: normalization and
                        performance metrics
