Illumina 450 methylation array normalization and metrics

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Documentation for package ‘wateRmelon’ version 1.24.0

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

-- A --

adaptRefQuantiles Functions from 450-pipeline (Touleimat & Tost)
agep Age Prediction from methylomic expression data
agep-method 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'

-- 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 --

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
estimateCellCounts.wmln Cell Proportion Estimation using wateRmelon
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
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

-- 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
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 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)
preprocessIlluminaMethylation Functions from 450-pipeline (Touleimat & Tost)
pwod Probe-Wise Outlier Detection
pwod-method Methods for Function 'pwod' in Package 'wateRmelon'

-- Q --

qual A measure of Normalization Violence

-- R --

readEPIC readEPIC
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
trafo Internal functions for readEPIC and other wateRmelon functions introduced in v 1.13.1

-- U --

uniqueAnnotationCategory Functions from 450-pipeline (Touleimat & Tost)

-- W --

wateRmelon Illumina 450K arrays: normalization and performance metrics