# Illumina 450 methylation array normalization and metrics

## Documentation for package ‘wateRmelon’ version 1.4.0

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

## Help Pages

A B C D F G I L M N P R S T U W

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

## -- A --

adaptRefQuantiles | Functions from 450-pipeline (Touleimat & Tost)
as.methylumi | Methods for Function 'as.methylumi'
as.methylumi-method | Methods for Function 'as.methylumi'
as.methylumi-methods | Methods for Function 'as.methylumi'

## -- 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
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

## -- C --

CheckBMIQ | Beta-Mixture Quantile (BMIQ) Normalisation method for Illumina 450k arrays
colnames-method | Methods for Function 'colnames' in Package 'wateRmelon'
colnames-methods | Methods for Function 'colnames' in Package 'wateRmelon'
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)
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
detectionPval.filter | Functions from 450-pipeline (Touleimat & Tost)
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'

## -- F --

filterXY | Functions from 450-pipeline (Touleimat & Tost)
findAnnotationProbes | Functions from 450-pipeline (Touleimat & Tost)
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
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
getColumns | Methods for Function 'as.methylumi'
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
got | Internal functions for Illumina i450 normalization functions

## -- I --

iDMR | Imprinting differentially methylated region probes of Illumina 450 arrays

## -- 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
metrics | Calculate a full set of 450K normalization/performance metrics

## -- 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)
normalize.quantiles2 | Functions from 450-pipeline (Touleimat & Tost)
normalizeIlluminaMethylation | Functions from 450-pipeline (Touleimat & Tost)

## -- P --

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)
pop | Internal functions for Illumina i450 normalization functions
preprocessIlluminaMethylation | Functions from 450-pipeline (Touleimat & Tost)

## -- R --

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'
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)
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 --

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

## -- U --

uniqueAnnotationCategory | Functions from 450-pipeline (Touleimat & Tost)

## -- W --

wateRmelon | Illumina 450K arrays: normalization and performance metrics