Handle Illumina methylation data

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Documentation for package ‘methylumi’ version 2.26.0

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B C D E F G H I L M N P Q S T U V misc

methylumi-package Handle Illumina methylation data

-- B --

betas methylumi accessors
betas-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
betas-method Class '"MethyLumiSet"' for containing Illumina methylation data
betas-method Generics defined in methylumi
betas<- methylumi accessors
betas<--method Class '"MethyLumiSet"' for containing Illumina methylation data
boxplot-method Class '"MethyLumiSet"' for containing Illumina methylation data

-- C --

combine-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
combine-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
combine-method Class '"MethyLumiSet"' for containing Illumina methylation data
combine27k450k Generics defined in methylumi
combine27k450k-method Class '"MethyLumiSet"' for containing Illumina methylation data
controlData Generics defined in methylumi
controlData-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
controlData-method Class '"MethyLumiSet"' for containing Illumina methylation data
controlData<- Generics defined in methylumi
controlData<-,MethyLumiSet Class '"MethyLumiSet"' for containing Illumina methylation data
controlData<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
controlData<--method Class '"MethyLumiQC"' for holding Illumina methylation QC data
controlTypes Methods for dealing with control data for Illumina methylation data.
controlTypes-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
controlTypes-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
controlTypes-method Class '"MethyLumiSet"' for containing Illumina methylation data
corplot methylumi accessors
corplot-method Class '"MethyLumiSet"' for containing Illumina methylation data
CpGs Data frame describing loci on the 27 and 450k arrays.
cy3 Generics defined in methylumi
Cy3.N Generics defined in methylumi
Cy3.N-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
Cy3.N-method Class '"MethyLumiSet"' for containing Illumina methylation data
Cy3<- Generics defined in methylumi
Cy3<--method Class '"MethyLumiQC"' for holding Illumina methylation QC data
cy5 Generics defined in methylumi
Cy5.N Generics defined in methylumi
Cy5.N-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
Cy5.N-method Class '"MethyLumiSet"' for containing Illumina methylation data
Cy5<- Generics defined in methylumi
Cy5<--method Class '"MethyLumiQC"' for holding Illumina methylation QC data

-- D --

dataType Generics defined in methylumi
dataType-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
dataType<- Generics defined in methylumi
dataType<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
designIItoMandU Generics defined in methylumi
designItoMandU Generics defined in methylumi
detection Generics defined in methylumi
detection-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
detection<- Generics defined in methylumi
detection<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
diagnostics Generics defined in methylumi
diagnostics-method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM

-- E --

estimateM Estimate methylation M-value matrix
exprs-method Class '"MethyLumiSet"' for containing Illumina methylation data
extractBarcodeAndPosition Extract the Barcode and Position Information from Sentrix ID

-- F --

featureFilter Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
featureFilter-method Annotation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object

-- G --

getAssayDataNameSubstitutions Return a data.frame of AssayData name substitutions.
getBarcodes Generics defined in methylumi
getHistory methylumi accessors
getHistory-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
getHistory-method Class '"MethyLumiSet"' for containing Illumina methylation data
getProtocolData Generics defined in methylumi

-- H --

hist-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
hist-method Class '"MethyLumiSet"' for containing Illumina methylation data

-- I --

IDATsToDFs Generics defined in methylumi
IDATtoDF Generics defined in methylumi
intensities.IB Generics defined in methylumi
intensities.IB-method Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.M Generics defined in methylumi
intensities.M-method Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.OOB Generics defined in methylumi
intensities.OOB-method Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.OOB.allelic Generics defined in methylumi
intensities.OOB.allelic-method Class '"MethyLumiSet"' for containing Illumina methylation data
intensities.U Generics defined in methylumi
intensities.U-method Class '"MethyLumiSet"' for containing Illumina methylation data
intensitiesByChannel Generics defined in methylumi
intensitiesByChannel-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
intensitiesByChannel-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
intensitiesByChannel-method Class '"MethyLumiSet"' for containing Illumina methylation data

-- L --

lumiCSV Generics defined in methylumi
lumIDAT Generics defined in methylumi

-- M --

mergeProbeDesigns Generics defined in methylumi
methylated methylumi accessors
methylated-method The base class for storing Illumina Methylation data
methylated-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
methylated-method Class '"MethyLumiSet"' for containing Illumina methylation data
methylated-method Generics defined in methylumi
methylated.N Generics defined in methylumi
methylated.N-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated.N-method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
methylated.N<- Generics defined in methylumi
methylated.N<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated.N<--method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
methylated<- methylumi accessors
methylated<--method The base class for storing Illumina Methylation data
methylated<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
methylated<--method Class '"MethyLumiSet"' for containing Illumina methylation data
methylData-class Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
methylumi Handle Illumina methylation data
MethyLumi-class The base class for storing Illumina Methylation data
methylumi.bgcorr Generics defined in methylumi
methylumi.diagnostics Generics defined in methylumi
methylumiCSV Generics defined in methylumi
methylumIDAT methylumIDAT
MethyLumiM Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
MethyLumiM-class Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
MethyLumiQC-class Class '"MethyLumiQC"' for holding Illumina methylation QC data
methylumiR Load data from Illumina methylation platform
MethyLumiSet-class Class '"MethyLumiSet"' for containing Illumina methylation data
mldat Example SAM format Illumina methylation dataset

-- N --

NChannelSetToMethyLumiSet Generics defined in methylumi
negctls Generics defined in methylumi
negctls-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
negctls-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
negctls-method Class '"MethyLumiSet"' for containing Illumina methylation data
negctls.stderr Generics defined in methylumi
negctls.stderr-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
negctls.stderr-method Class '"MethyLumiSet"' for containing Illumina methylation data
negnorm Generics defined in methylumi
negnorm-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
negnorm-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
negnorm-method Class '"MethyLumiSet"' for containing Illumina methylation data
normalizeMethyLumiSet Normalize a MethyLumiSet, accounting for dye bias
normctls Generics defined in methylumi
normctls-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
normctls-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
normctls-method Class '"MethyLumiSet"' for containing Illumina methylation data

-- P --

pairs-method Class '"MethyLumiSet"' for containing Illumina methylation data
plotNAs Generics defined in methylumi
plotNAs-method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
plotNegOob Generics defined in methylumi
plotSampleIntensities Plot the sample intensities.
plotSampleIntensities-method Class '"MethyLumiSet"' for containing Illumina methylation data
probeNAs Generics defined in methylumi
probeNAs-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
probeNAs-method Class '"MethyLumiSet"' for containing Illumina methylation data
psummary Generics defined in methylumi
pval.detect Generics defined in methylumi
pval.detect-method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
pval.detect<- Generics defined in methylumi
pval.detect<--method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
pvals methylumi accessors
pvals-method The base class for storing Illumina Methylation data
pvals-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
pvals<- methylumi accessors
pvals<--method The base class for storing Illumina Methylation data

-- Q --

qc.probe.plot Generics defined in methylumi
QCdata methylumi accessors
QCdata-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
QCdata-method Class '"MethyLumiSet"' for containing Illumina methylation data
QCdata<- methylumi accessors
QCdata<-,MethyLumiSet Class '"MethyLumiSet"' for containing Illumina methylation data
QCdata<--method Class '"MethyLumiQC"' for holding Illumina methylation QC data
qcplot Methods for dealing with control data for Illumina methylation data.
qcplot-method The base class for storing Illumina Methylation data
qcplot-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
qcplot-method Class '"MethyLumiSet"' for containing Illumina methylation data

-- S --

sampleNAs Generics defined in methylumi
sampleNAs-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
sampleNAs-method Class '"MethyLumiSet"' for containing Illumina methylation data
show-method Class '"MethyLumiSet"' for containing Illumina methylation data
stripBeadNs Strip excessive probe-level data from MethyLumiSets
stripBeadSDs Strip excessive probe-level data from MethyLumiSets
stripMethyLumiSet Strip excessive probe-level data from MethyLumiSets
stripOOB Strip excessive probe-level data from MethyLumiSets
summary-method The base class for storing Illumina Methylation data

-- T --

total.intensity Generics defined in methylumi
total.intensity-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
total.intensity-method Class '"MethyLumiSet"' for containing Illumina methylation data

-- U --

unmethylated methylumi accessors
unmethylated-method The base class for storing Illumina Methylation data
unmethylated-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated-method Class '"MethyLumiQC"' for holding Illumina methylation QC data
unmethylated-method Class '"MethyLumiSet"' for containing Illumina methylation data
unmethylated-method Generics defined in methylumi
unmethylated.N Generics defined in methylumi
unmethylated.N-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated.N-method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
unmethylated.N<- Generics defined in methylumi
unmethylated.N<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated.N<--method Class '"methylData"', superclass for MethyLumiSet and MethyLumiM
unmethylated<- methylumi accessors
unmethylated<--method The base class for storing Illumina Methylation data
unmethylated<--method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
unmethylated<--method Class '"MethyLumiSet"' for containing Illumina methylation data

-- V --

varFilter Variation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object
varFilter-method Variation-based Filtering of Features (CpG sites) in a MethyLumiSet or MethyLumiM object

-- misc --

[-method Class "MethyLumiM": for Illumina Methylation microarray data using logRatios
[-method Class '"MethyLumiSet"' for containing Illumina methylation data