B C D E F G H I L M N P Q R S T U V misc
methylumi-package | Handle Illumina methylation data |
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 |
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 |
compare.chips | Generics defined in methylumi |
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 |
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 |
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 |
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 |
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 |
hist-method | Class '"MethyLumiQC"' for holding Illumina methylation QC data |
hist-method | Class '"MethyLumiSet"' for containing Illumina methylation data |
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 |
lumiCSV | Generics defined in methylumi |
lumIDAT | Generics defined in methylumi |
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 |
methylumiMU | methylumiMU |
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 |
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 |
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 |
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 |
readMethyLumIDAT | Generics defined in methylumi |
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 |
subset27kas450k | Generics defined in methylumi |
subset450kas27k | Generics defined in methylumi |
subsetCommonProbes | Generics defined in methylumi |
summary-method | The base class for storing Illumina Methylation data |
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 |
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 |
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 |
[-method | Class "MethyLumiM": for Illumina Methylation microarray data using logRatios |
[-method | Class '"MethyLumiSet"' for containing Illumina methylation data |