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 |