minfi-package | Analyze Illumina's methylation arrays |
annotation-method | GenomicMethylSet instances |
bgcorrect.illumina | Perform preprocessing as Genome Studio. |
controlStripPlot | Plot control probe signals. |
densityBeanPlot | Density bean plots of methylation Beta values. |
densityPlot | Density plots of methylation Beta values. |
detectionP | Detection p-values for all probed genomic positions. |
dmpFinder | Find differentially methylated positions |
dropMethylationLoci | MethylSet instances |
featureNames-method | GenomicMethylSet instances |
GenomicMethylSet | GenomicMethylSet instances |
GenomicMethylSet-class | GenomicMethylSet instances |
getBeta | MethylSet instances |
getBeta-method | GenomicMethylSet instances |
getBeta-method | MethylSet instances |
getBeta-method | Class '"RGChannelSet"' |
getControlAddress | Class '"IlluminaMethylationManifest"' |
getControlTypes | Class '"IlluminaMethylationManifest"' |
getGreen | Class '"RGChannelSet"' |
getLocations | Class 'IlluminaMethylationAnnotation' |
getLocations-method | Class 'IlluminaMethylationAnnotation' |
getLocations-method | MethylSet instances |
getM | MethylSet instances |
getM-method | GenomicMethylSet instances |
getM-method | MethylSet instances |
getManifest | Class '"IlluminaMethylationManifest"' |
getManifest-method | Class 'IlluminaMethylationAnnotation' |
getManifest-method | Class '"IlluminaMethylationManifest"' |
getManifest-method | MethylSet instances |
getManifest-method | Class '"RGChannelSet"' |
getManifestInfo | Class '"IlluminaMethylationManifest"' |
getMeth | MethylSet instances |
getMeth-method | GenomicMethylSet instances |
getMeth-method | MethylSet instances |
getProbeInfo | Class '"IlluminaMethylationManifest"' |
getRed | Class '"RGChannelSet"' |
getUnmeth | MethylSet instances |
getUnmeth-method | GenomicMethylSet instances |
getUnmeth-method | MethylSet instances |
IlluminaMethylationAnnotation | Class 'IlluminaMethylationAnnotation' |
IlluminaMethylationAnnotation-class | Class 'IlluminaMethylationAnnotation' |
IlluminaMethylationManifest | Class '"IlluminaMethylationManifest"' |
IlluminaMethylationManifest-class | Class '"IlluminaMethylationManifest"' |
ilogit2 | logit in base 2. |
initialize-method | MethylSet instances |
initialize-method | Class '"RGChannelSet"' |
logit2 | logit in base 2. |
mapToGenome | Mapping methylation data to the genome |
mapToGenome-method | Mapping methylation data to the genome |
mapToGenome-methods | Mapping methylation data to the genome |
mdsPlot | Multi-dimensional scaling plots giving an overview of similarities and differences between samples. |
MethylSet | MethylSet instances |
MethylSet-class | MethylSet instances |
minfi | Analyze Illumina's methylation arrays |
normalize.illumina.control | Perform preprocessing as Genome Studio. |
pData-method | GenomicMethylSet instances |
plotBetasByType | Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types. |
plotCpg | Plot methylation values at an single genomic position |
preprocessIllumina | Perform preprocessing as Genome Studio. |
preprocessMethod | MethylSet instances |
preprocessMethod-method | GenomicMethylSet instances |
preprocessMethod-method | MethylSet instances |
preprocessRaw | Creation of a MethylSet without normalization |
preprocessSWAN | Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips |
qcReport | QC report for Illumina Infinium Human Methylation 450k arrays |
read.450k | Parsing IDAT files from Illumina methylation arrays. |
read.450k.exp | Reads an entire 450k experiment using a sample sheet |
read.450k.sheet | Reading an Illumina methylation sample sheet |
RGChannelSet | Class '"RGChannelSet"' |
RGChannelSet-class | Class '"RGChannelSet"' |
RGChannelSetExtended | Class '"RGChannelSet"' |
RGChannelSetExtended-class | Class '"RGChannelSet"' |
sampleNames-method | GenomicMethylSet instances |
show-method | GenomicMethylSet instances |
show-method | Class 'IlluminaMethylationAnnotation' |
show-method | Class '"IlluminaMethylationManifest"' |
show-method | MethylSet instances |
show-method | Class '"RGChannelSet"' |