Handle Illumina methylation data


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Documentation for package ‘methylumi’ version 1.0.0

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methylumi-package Handle Illumina methylation data
betas methylumi accessors
betas,MethyLumiSet-method Class to hold Illumina Methylation data
betas<- methylumi accessors
betas<-,MethyLumiSet,matrix-method Class to hold Illumina Methylation data
boxplot,MethyLumiSet-method Class to hold Illumina Methylation data
combine,MethyLumiSet,MethyLumiSet-method Class to hold Illumina Methylation data
controlTypes Methods for dealing with control data for Illumina methylation data.
controlTypes,MethyLumiQC-method Class to hold Illumina Methylation QC data
controlTypes,MethyLumiSet-method Class to hold Illumina Methylation data
corplot,MethyLumiSet-method Class to hold Illumina Methylation data
exprs,MethyLumiQC-method Class to hold Illumina Methylation QC data
exprs,MethyLumiSet-method Class to hold Illumina Methylation data
exprs<-,MethyLumiQC,matrix-method Class to hold Illumina Methylation QC data
exprs<-,MethyLumiSet,matrix-method Class to hold Illumina Methylation data
extractBarcodeAndPosition Extract the Barcode and Position Information from Sentrix ID
getAssayDataNameSubstitutions Return a data.frame of AssayData name substitutions.
getHistory methylumi accessors
getHistory,MethyLumiSet-method Class to hold Illumina Methylation data
hist,MethyLumiSet-method Class to hold Illumina Methylation data
initialize,MethyLumiQC-method Class to hold Illumina Methylation QC data
initialize,MethyLumiSet-method Class to hold Illumina Methylation data
methylated methylumi accessors
methylated,MethyLumi-method The base class for storing Illumina Methylation data
methylated,MethyLumiSet-method Class to hold Illumina Methylation data
methylated<- methylumi accessors
methylated<-,MethyLumi,matrix-method The base class for storing Illumina Methylation data
methylated<-,MethyLumiSet,matrix-method Class to hold Illumina Methylation data
methylumi Handle Illumina methylation data
MethyLumi-class The base class for storing Illumina Methylation data
MethyLumiQC-class Class to hold Illumina Methylation QC data
methylumiR Load data from Illumina methylation platform
MethyLumiSet-class Class to hold Illumina Methylation data
mldat Example SAM format Illumina methylation dataset
normalizeMethyLumiSet Normalize a MethyLumiSet, accounting for dye bias
pairs,MethyLumiSet-method Class to hold Illumina Methylation data
plotSampleIntensities Plot the sample intensities.
plotSampleIntensities,MethyLumiSet-method Class to hold Illumina Methylation data
pvals methylumi accessors
pvals,MethyLumi-method The base class for storing Illumina Methylation data
pvals<- methylumi accessors
pvals<-,MethyLumi,matrix-method The base class for storing Illumina Methylation data
QCdata methylumi accessors
QCdata,MethyLumiSet-method Class to hold Illumina Methylation data
QCdata<- methylumi accessors
QCdata<-,MethyLumiSet,MethyLumiQC-method Class to hold Illumina Methylation data
QCDataOrNULL-class Class to hold Illumina Methylation QC data
qcplot Methods for dealing with control data for Illumina methylation data.
qcplot,Methylumi-method The base class for storing Illumina Methylation data
qcplot,MethyLumiQC-method Class to hold Illumina Methylation QC data
qcplot,MethyLumiSet-method Class to hold Illumina Methylation data
show,MethyLumiSet-method Class to hold Illumina Methylation data
summary,MethyLumi-method The base class for storing Illumina Methylation data
unmethylated methylumi accessors
unmethylated,MethyLumi-method The base class for storing Illumina Methylation data
unmethylated,MethyLumiSet-method Class to hold Illumina Methylation data
unmethylated<- methylumi accessors
unmethylated<-,MethyLumi,matrix-method The base class for storing Illumina Methylation data
unmethylated<-,MethyLumiSet,matrix-method Class to hold Illumina Methylation data
[,MethyLumiSet-method Class to hold Illumina Methylation data