Illumina 450 methylation array normalization and metrics


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Documentation for package ‘wateRmelon’ version 1.10.0

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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