minfi-package | Analyze Illumina's methylation arrays |
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 |
getAnno | Class MethylSet |
getBeta | Class MethylSet |
getControlAddress | Utility functions for retrieving array design information for Illumina methylation microarrays. |
getGreen | Class '"RGChannelSet"' |
getM | Class MethylSet |
getManifest | Class '"RGChannelSet"' |
getManifestInfo | Utility functions for retrieving array design information for Illumina methylation microarrays. |
getMeth | Class MethylSet |
getProbeData | Utility functions for retrieving array design information for Illumina methylation microarrays. |
getProbeInfo | Utility functions for retrieving array design information for Illumina methylation microarrays. |
getRed | Class '"RGChannelSet"' |
getUnmeth | Class MethylSet |
IlluminaMethylationAnnotation-class | Class '"IlluminaMethylationAnnotation"' |
IlluminaMethylationManifest-class | Class '"IlluminaMethylationManifest"' |
ilogit2 | logit in base 2. |
initialize-method | Class MethylSet |
initialize-method | Class '"RGChannelSet"' |
logit2 | logit in base 2. |
manifestNew | Class '"IlluminaMethylationManifest"' |
mdsPlot | Multi-dimensional scaling plots giving an overview of similarities and differences between samples. |
MethylSet | Class MethylSet |
MethylSet-class | Class MethylSet |
minfi | Analyze Illumina's methylation arrays |
normalize.illumina.control | Perform preprocessing as Genome Studio. |
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. |
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"' |
show-method | Class '"IlluminaMethylationAnnotation"' |
show-method | Class '"IlluminaMethylationManifest"' |
show-method | Class MethylSet |
show-method | Class '"RGChannelSet"' |