schalkwyk/wateRmelon
Illumina DNA methylation array normalization and metrics

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366
Source code
84
Man pages
50
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schalkwyk/wateRmelon: Illumina DNA methylation array normalization and metrics
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API

API for schalkwyk/wateRmelon
Illumina DNA methylation array normalization and metrics

Global functions
.adjusted_normalizeFunnorm450k Source code
.buildControlMatrix450k Source code
.calculate_age Source code
.compute_ages Source code
.createAnnotation Man page Source code
.extractFromRGSet450k Source code
.getFunnormIndices Source code
.getManifestString Man page Source code
.handle_missing Source code
.impose Source code
.isGenomicOrStop Source code
.isMatrixBacked Source code
.isMatrixBackedOrStop Source code
.isRGOrStop Source code
.normalizeMatrix Source code
.normalizeQuantiles2 Source code
.regularizeQuantiles Source code
.returnFit Source code
.returnFitBySex Source code
.split_intercept_from_coeff Source code
BMIQ Man page Source code
BMIQ,ANY-method Man page
BMIQ,MethyLumiSet-method Man page
BMIQ,MethylSet-method Man page
BMIQ-methods Man page
Beta2M Man page
CheckBMIQ Man page Source code
DataToNChannelSet2 Man page Source code
IDATsToMatrices2 Man page Source code
IDATtoMatrix2 Man page Source code
M2Beta Man page
NChannelSetToMethyLumiSet2 Man page Man page Source code
adaptRefQuantiles Man page Source code
adjustedDasen Man page Source code
adjustedFunnorm Man page Source code
age_coefficients Man page
agep Man page Source code
agep,MethyLumiSet-method Man page
agep,MethylSet-method Man page
agep,RGChannelSet-method Man page
anSNP Man page Source code
anti.trafo Man page Source code
aoget Man page Source code Source code
as.methylumi Man page Source code
as.methylumi,ANY-method Man page
as.methylumi,MethyLumiSet-method Man page
as.methylumi,MethylSet-method Man page
as.methylumi-methods Man page
auc_probability Man page Source code
beadc Man page Source code
beadcount Man page Source code
betaqn Man page Source code
betaqn,MethyLumiSet-method Man page
betaqn,MethylSet-method Man page
betaqn,RGChannelSet-method Man page
betaqn,exprmethy450-method Man page
bfp Man page Source code
bgIntensitySwan.methylumi Man page
bscon Man page Source code
bscon,MethyLumiSet-method Man page
bscon,RGChannelSet-method Man page
bscon_methy Man page Source code
bscon_minfi Man page Source code
canno Man page
coRankedMatrices Man page Source code
coef Man page
colnames,MethyLumiSet-method Man page
colnames-methods Man page
columnMatrix Man page Source code
combo Man page
concatenateMatrices Man page Source code
correctI Man page
correctII Man page
danen Man page
danen,MethyLumiSet-method Man page
danen,MethylSet-method Man page
danen,RGChannelSet-method Man page
danes Man page Source code
danes,MethyLumiSet-method Man page
danes,MethylSet-method Man page
danes,RGChannelSet-method Man page
danet Man page Source code
danet,MethyLumiSet-method Man page
danet,MethylSet-method Man page
danet,RGChannelSet-method Man page
dasen Man page Source code
dasen,MethyLumiSet-method Man page
dasen,MethylSet-method Man page
dasen,RGChannelSet-method Man page
dataDetectPval2NA Man page Source code
daten1 Man page Source code
daten1,MethyLumiSet-method Man page
daten1,MethylSet-method Man page
daten1,RGChannelSet-method Man page
daten2 Man page Source code
daten2,MethyLumiSet-method Man page
daten2,MethylSet-method Man page
daten2,RGChannelSet-method Man page
db1 Man page Source code
designIItoMandU2 Man page Source code
designItoMandU2 Man page Source code
detectP Source code
detectionPval.filter Man page Source code
dfort Man page Source code
dfs2 Man page Source code
dfsfit Man page Source code
dmrse Man page Source code
dmrse,MethyLumiSet-method Man page
dmrse,MethylSet-method Man page
dmrse,RGChannelSet-method Man page
dmrse,exprmethy450-method Man page
dmrse-methods Man page
dmrse_col Man page Source code
dmrse_col,MethyLumiSet-method Man page
dmrse_col,MethylSet-method Man page
dmrse_col,RGChannelSet-method Man page
dmrse_col,exprmethy450-method Man page
dmrse_col-methods Man page
dmrse_row Man page Source code
dmrse_row,MethyLumiSet-method Man page
dmrse_row,MethylSet-method Man page
dmrse_row,RGChannelSet-method Man page
dmrse_row,exprmethy450-method Man page
dmrse_row-methods Man page
epic.controls Man page
epicv2clean Man page Source code
epicv2clean.default Man page Source code
epicv2clean.gds.class Man page
estimateCellCounts.wateRmelon Man page
estimateCellCounts.wateRmelon,MethyLumiSet-method Man page
estimateCellCounts.wateRmelon,MethylSet-method Man page
estimateCellCounts.wateRmelon,RGChannelSet-method Man page
estimateCellCounts.wmln Man page Source code
estimateSex Man page Source code
extractAssayDataFromList2 Man page Source code
filterXY Man page Source code
findAnnotationProbes Man page Source code
fot Man page Man page Source code
fuks Man page
fuks,MethyLumiSet-method Man page
fuks,MethylSet-method Man page
fuks,RGChannelSet-method Man page
fuks,exprmethy450-method Man page
gcoms Man page Source code
gcose Man page Source code
genall Man page Source code
generateManifest Man page Source code
genki Man page Source code
genki,MethyLumiSet-method Man page
genki,MethylSet-method Man page
genki,RGChannelSet-method Man page
genki,exprmethy450-method Man page
genki-methods Man page
genkme Man page Source code
genkus Man page Source code
genme Man page
genus Man page Source code
getColumns Man page
getControlProbes2 Man page Source code
getMethylationBeadMappers2 Man page Source code
getMethylumiBeta Man page Source code
getQuantiles Man page Source code
getSamples Man page Source code
getsnp Man page Source code
goodSNP Man page Source code
got Man page Man page Source code
hannumCoef Man page
iDMR Man page
idet Man page Source code
iqrFun Man page Source code
loadMethylumi2 Man page Source code
lumiMethyR2 Man page
melon Man page
mergeProbeDesigns2 Man page Source code
methylumIDATepic Man page Source code
metrics Man page Source code
mvFun Man page Source code
nanes Man page Source code
nanes,MethyLumiSet-method Man page
nanes,MethylSet-method Man page
nanes,RGChannelSet-method Man page
nanet Man page Source code
nanet,MethyLumiSet-method Man page
nanet,MethylSet-method Man page
nanet,RGChannelSet-method Man page
nasen Man page
nasen,MethyLumiSet-method Man page
nasen,MethylSet-method Man page
nasen,RGChannelSet-method Man page
naten Man page
naten,MethyLumiSet-method Man page
naten,MethylSet-method Man page
naten,RGChannelSet-method Man page
nbBeadsFilter Man page Source code
normalize.quantiles2 Man page Source code
normalizeIlluminaMethylation Man page Source code
outlyx Man page Source code
outlyx,MethyLumiSet-method Man page
outlyx,MethylSet-method Man page
outlyx,RGChannelSet-method Man page
oxyscale Man page
p_dfsfit Man page
pcouted Man page Source code
pfilter Man page
pfilter,MethyLumiSet-method Man page
pfilter,RGChannelSetExtended-method Man page
pfilter-methods Man page
pipelineIlluminaMethylation.batch Man page Source code
plot_predicted_sex Man page Source code
pop Man page Man page
preprocessIlluminaMethylation Man page Source code
pwod Man page Source code
pwod,MethyLumiSet-method Man page
pwod,MethylSet-method Man page
pwod,RGChannelSet-method Man page
qual Man page Source code
read.manifest Man page Source code
readEPIC Man page Source code
readPepo Man page
referenceQuantiles Man page Source code
robustQuantileNorm_Illumina450K Man page Source code
robustQuantileNorm_Illumina450K.probeCategories Man page Source code
seabi Man page
seabi,MethyLumiSet-method Man page
seabi,MethylSet-method Man page
seabi,RGChannelSet-method Man page
seabi,exprmethy450-method Man page
seabi-methods Man page
seabi2 Man page
seabird Man page Source code
seabird2 Man page Source code
sextest Man page Source code
smokp Man page Source code
smokp,MethyLumiSet-method Man page
smokp,MethylSet-method Man page
smokp,RGChannelSet-method Man page
smokp_cpgs Man page
sort_order Man page Source code
subbo Man page Source code
summits Man page
swan Man page
swan,MethyLumiSet-method Man page
swan,MethylSet-method Man page
swan,RGChannelSet-method Man page
tie_norm Man page Source code
tost Man page Source code
tost,MethyLumiSet-method Man page
tost,MethylSet-method Man page
tost,RGChannelSet-method Man page
trafo Man page Source code
uSexQN Man page Source code
uSexQN,MethyLumiSet-method Man page
uSexQN,MethylSet-method Man page
uSexQN,RGChannelSet-method Man page
uSexQNengine Man page Source code
uniqueAnnotationCategory Man page Source code
wateRmelon Man page
wateRmelon-package Man page
schalkwyk/wateRmelon documentation built on Aug. 13, 2024, 9:52 a.m.

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