minfi-package | Analyze Illumina's methylation arrays |
addQC | Estimate sample-specific quality control (QC) for methylation data |
addSex | Estimating sample sex based on methylation data |
addSnpInfo | Accessing annotation for Illumina methylation objects |
annotation-method | GenomicMethylSet instances |
annotation-method | GenomicRatioSet instances |
annotation-method | MethylSet instances |
annotation-method | Class '"RGChannelSet"' |
annotation-method | RatioSet instances |
annotation<--method | GenomicMethylSet instances |
annotation<--method | GenomicRatioSet instances |
annotation<--method | MethylSet instances |
annotation<--method | Class '"RGChannelSet"' |
annotation<--method | RatioSet instances |
bgcorrect.illumina | Perform preprocessing as Genome Studio. |
blockFinder | Finds blocks of methylation differences for Illumina methylation arrays |
bumphunter-method | Methods for function 'bumphunter' in Package 'minfi' |
coerce-method | Class '"RGChannelSet"' |
combine-method | GenomicMethylSet instances |
combine-method | GenomicRatioSet instances |
combine-method | MethylSet instances |
combine-method | Class '"RGChannelSet"' |
combine-method | RatioSet instances |
combineArrays | A method for combining different types of methylation arrays into a virtual array. |
combineArrays-method | A method for combining different types of methylation arrays into a virtual array. |
compartments | Estimates A/B compartments from Illumina methylation arrays |
controlStripPlot | Plot control probe signals. |
convertArray | A method for converting a type of methylation arrays into a virtual array of another type. |
convertArray-method | A method for converting a type of methylation arrays into a virtual array of another type. |
cpgCollapse | Collapse methylation values of adjacent CpGs into a summary value. |
createCorMatrix | Estimates A/B compartments from Illumina methylation arrays |
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 |
dropLociWithSnps | Accessing annotation for Illumina methylation objects |
dropMethylationLoci | MethylSet instances |
estimateCellCounts | Cell Proportion Estimation |
extractAB | Estimates A/B compartments from Illumina methylation arrays |
featureNames-method | GenomicMethylSet instances |
featureNames-method | GenomicRatioSet instances |
featureNames-method | MethylSet instances |
featureNames-method | Class '"RGChannelSet"' |
featureNames-method | RatioSet instances |
featureNames<--method | GenomicMethylSet instances |
featureNames<--method | GenomicRatioSet instances |
featureNames<--method | MethylSet instances |
featureNames<--method | Class '"RGChannelSet"' |
featureNames<--method | RatioSet instances |
fixMethOutliers | Fix methylation outliers |
gaphunter | Find gap signals in 450k data |
GenomicMethylSet | GenomicMethylSet instances |
GenomicMethylSet-class | GenomicMethylSet instances |
GenomicRatioSet | GenomicRatioSet instances |
GenomicRatioSet-class | GenomicRatioSet instances |
getAnnotation | Accessing annotation for Illumina methylation objects |
getAnnotationObject | Accessing annotation for Illumina methylation objects |
getBeta | MethylSet instances |
getBeta-method | GenomicMethylSet instances |
getBeta-method | GenomicRatioSet instances |
getBeta-method | MethylSet instances |
getBeta-method | Class '"RGChannelSet"' |
getBeta-method | RatioSet instances |
getCN | GenomicRatioSet instances |
getCN-method | GenomicMethylSet instances |
getCN-method | GenomicRatioSet instances |
getCN-method | MethylSet instances |
getCN-method | RatioSet instances |
getControlAddress | Class '"IlluminaMethylationManifest"' |
getGenomicRatioSetFromGEO | Reading Illumina methylation array data from GEO. |
getGreen | Class '"RGChannelSet"' |
getIslandStatus | Accessing annotation for Illumina methylation objects |
getLocations | Accessing annotation for Illumina methylation objects |
getM | MethylSet instances |
getM-method | GenomicMethylSet instances |
getM-method | GenomicRatioSet instances |
getM-method | MethylSet instances |
getM-method | RatioSet 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 |
getMethSignal | Various utilities |
getNBeads | Class '"RGChannelSet"' |
getOOB | Class '"RGChannelSet"' |
getProbeInfo | Class '"IlluminaMethylationManifest"' |
getProbeType | Accessing annotation for Illumina methylation objects |
getQC | Estimate sample-specific quality control (QC) for methylation data |
getRed | Class '"RGChannelSet"' |
getSex | Estimating sample sex based on methylation data |
getSnpBeta | Class '"RGChannelSet"' |
getSnpInfo | Accessing annotation for Illumina methylation objects |
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. |
logit2 | logit in base 2. |
makeGenomicRatioSetFromMatrix | Make a GenomicRatioSet from a matrix |
mapToGenome | Mapping methylation data to the genome |
mapToGenome-method | GenomicMethylSet instances |
mapToGenome-method | GenomicRatioSet instances |
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 |
minfi-defunct | Defunct functions in package 'minfi' |
minfi-deprecated | Deprecated functions in package 'minfi' |
minfiQC | easy one-step QC of methylation object |
normalize.illumina.control | Perform preprocessing as Genome Studio. |
pData-method | GenomicMethylSet instances |
pData-method | GenomicRatioSet instances |
pData-method | MethylSet instances |
pData-method | Class '"RGChannelSet"' |
pData-method | RatioSet instances |
pData<--method | GenomicMethylSet instances |
pData<--method | GenomicRatioSet instances |
pData<--method | MethylSet instances |
pData<--method | Class '"RGChannelSet"' |
pData<--method | RatioSet 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 |
plotQC | Estimate sample-specific quality control (QC) for methylation data |
plotSex | Estimating sample sex based on methylation data |
preprocessFunnorm | Functional normalization for Illumina 450k arrays |
preprocessIllumina | Perform preprocessing as Genome Studio. |
preprocessMethod | MethylSet instances |
preprocessMethod-method | GenomicMethylSet instances |
preprocessMethod-method | GenomicRatioSet instances |
preprocessMethod-method | MethylSet instances |
preprocessMethod-method | RatioSet instances |
preprocessNoob | The Noob/ssNoob preprocessing method for Infinium methylation microarrays. |
preprocessQuantile | Stratified quantile normalization for an Illumina methylation array. |
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 |
ratioConvert | Converting methylation signals to ratios (Beta or M-values) |
ratioConvert-method | Converting methylation signals to ratios (Beta or M-values) |
ratioConvert-methods | Converting methylation signals to ratios (Beta or M-values) |
RatioSet | RatioSet instances |
RatioSet-class | RatioSet instances |
read.450k | Defunct functions in package 'minfi' |
read.450k.exp | Defunct functions in package 'minfi' |
read.450k.sheet | Defunct functions in package 'minfi' |
read.metharray | Parsing IDAT files from Illumina methylation arrays. |
read.metharray.exp | Reads an entire metharray experiment using a sample sheet |
read.metharray.sheet | Reading an Illumina methylation sample sheet |
readGEORawFile | Read in Unmethylated and Methylated signals from a GEO raw file. |
readTCGA | Read in tab deliminited file in the TCGA format |
RGChannelSet | Class '"RGChannelSet"' |
RGChannelSet-class | Class '"RGChannelSet"' |
RGChannelSetExtended | Class '"RGChannelSet"' |
RGChannelSetExtended-class | Class '"RGChannelSet"' |
sampleNames-method | GenomicMethylSet instances |
sampleNames-method | GenomicRatioSet instances |
sampleNames-method | MethylSet instances |
sampleNames-method | Class '"RGChannelSet"' |
sampleNames-method | RatioSet instances |
sampleNames<--method | GenomicMethylSet instances |
sampleNames<--method | GenomicRatioSet instances |
sampleNames<--method | MethylSet instances |
sampleNames<--method | Class '"RGChannelSet"' |
sampleNames<--method | RatioSet instances |
show-method | GenomicMethylSet instances |
show-method | GenomicRatioSet instances |
show-method | Class 'IlluminaMethylationAnnotation' |
show-method | Class '"IlluminaMethylationManifest"' |
show-method | MethylSet instances |
show-method | Class '"RGChannelSet"' |
show-method | RatioSet instances |
subsetByLoci | Subset an RGChannelset by CpG loci. |