Handle Illumina methylation data


[Up] [Top]

Documentation for package ‘methylumi’ version 1.8.0

Help Pages

methylumi-package Handle Illumina methylation data
betas methylumi accessors
betas-method Class to hold Illumina Methylation data
betas<- methylumi accessors
betas<--method Class to hold Illumina Methylation data
boxplot-method Class to hold Illumina Methylation data
coerce-method Class "MethyLumiM": for Illumina Methylation microarray data
combine-method Class "MethyLumiM": for Illumina Methylation microarray data
combine-method Class to hold Illumina Methylation data
controlData Class "MethyLumiM": for Illumina Methylation microarray data
controlData-method Class "MethyLumiM": for Illumina Methylation microarray data
controlData<- Class "MethyLumiM": for Illumina Methylation microarray data
controlData<--method Class "MethyLumiM": for Illumina Methylation microarray data
controlTypes Methods for dealing with control data for Illumina methylation data.
controlTypes-method Class to hold Illumina Methylation QC data
controlTypes-method Class to hold Illumina Methylation data
corplot methylumi accessors
corplot-method Class to hold Illumina Methylation data
detection Class "MethyLumiM": for Illumina Methylation microarray data
detection-method Class "MethyLumiM": for Illumina Methylation microarray data
detection<- Class "MethyLumiM": for Illumina Methylation microarray data
detection<--method Class "MethyLumiM": for Illumina Methylation microarray data
estimateM Estimate methylation M-value matrix
exprs-method Class to hold Illumina Methylation QC data
exprs-method Class to hold Illumina Methylation data
exprs<--method Class to hold Illumina Methylation QC data
exprs<--method Class to hold 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.
getHistory methylumi accessors
getHistory-method Class "MethyLumiM": for Illumina Methylation microarray data
getHistory-method Class to hold Illumina Methylation data
hist-method Class to hold Illumina Methylation data
initialize-method Class "MethyLumiM": for Illumina Methylation microarray data
initialize-method Class to hold Illumina Methylation QC data
initialize-method Class to hold Illumina Methylation data
methylated methylumi accessors
methylated-method The base class for storing Illumina Methylation data
methylated-method Class "MethyLumiM": for Illumina Methylation microarray data
methylated-method Class to hold Illumina Methylation data
methylated.N Class "MethyLumiM": for Illumina Methylation microarray data
methylated.N-method Class "MethyLumiM": for Illumina Methylation microarray data
methylated.N<- Class "MethyLumiM": for Illumina Methylation microarray data
methylated.N<--method Class "MethyLumiM": for Illumina Methylation microarray data
methylated<- methylumi accessors
methylated<--method The base class for storing Illumina Methylation data
methylated<--method Class "MethyLumiM": for Illumina Methylation microarray data
methylated<--method Class to hold Illumina Methylation data
methylumi Handle Illumina methylation data
MethyLumi-class The base class for storing Illumina Methylation data
MethyLumiM-class Class "MethyLumiM": for Illumina Methylation microarray 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-method Class to hold Illumina Methylation data
plotSampleIntensities Plot the sample intensities.
plotSampleIntensities-method Class to hold Illumina Methylation data
pvals methylumi accessors
pvals-method The base class for storing Illumina Methylation data
pvals<- methylumi accessors
pvals<--method The base class for storing Illumina Methylation data
QCdata methylumi accessors
QCdata-method Class to hold Illumina Methylation data
QCdata<- methylumi accessors
QCdata<--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-method The base class for storing Illumina Methylation data
qcplot-method Class to hold Illumina Methylation QC data
qcplot-method Class to hold Illumina Methylation data
show-method Class to hold Illumina Methylation data
summary-method The base class for storing 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
unmethylated-method Class to hold Illumina Methylation data
unmethylated.N Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated.N-method Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated.N<- Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated.N<--method Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated<- methylumi accessors
unmethylated<--method The base class for storing Illumina Methylation data
unmethylated<--method Class "MethyLumiM": for Illumina Methylation microarray data
unmethylated<--method Class to hold 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
[-method Class to hold Illumina Methylation data