Illumina DNA methylation array normalization and metrics

Documentation for package ‘wateRmelon’ version 2.15.0

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

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