minfi: Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

AuthorKasper Daniel Hansen [cre, aut], Martin Aryee [aut], Rafael A. Irizarry [aut], Andrew E. Jaffe [ctb], Jovana Maksimovic [ctb], E. Andres Houseman [ctb], Jean-Philippe Fortin [ctb], Tim Triche [ctb], Shan V. Andrews [ctb]
Date of publicationNone
MaintainerKasper Daniel Hansen <kasperdanielhansen@gmail.com>
LicenseArtistic-2.0
Version1.20.2
https://github.com/kasperdanielhansen/minfi

View on Bioconductor

Man pages

blockFinder: Finds blocks of methylation differences for Illumina...

bumphunter: Methods for function 'bumphunter' in Package 'minfi'

combineArrays: A method for combining different types of methylation arrays...

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...

cpgCollapse: Collapse methylation values of adjacent CpGs into a summary...

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

estimateCellCounts: Cell Proportion Estimation

fixMethOutliers: Fix methylation outliers

gaphunter: Find gap signals in 450k data

GenomicMethylSet-class: GenomicMethylSet instances

GenomicRatioSet-class: GenomicRatioSet instances

getAnnotation: Accessing annotation for Illumina methylation objects

getGenomicRatioSetFromGEO: Reading Illumina methylation array data from GEO.

getQC: Estimate sample-specific quality control (QC) for methylation...

getSex: Estimating sample sex based on methylation data

IlluminaMethylationAnnotation-class: Class 'IlluminaMethylationAnnotation'

IlluminaMethylationManifest-class: Class '"IlluminaMethylationManifest"'

logit2: logit in base 2.

makeGenomicRatioSetFromMatrix: Make a GenomicRatioSet from a matrix

mapToGenome-methods: Mapping methylation data to the genome

mdsPlot: Multi-dimensional scaling plots giving an overview of...

MethylSet-class: MethylSet instances

minfi-defunct: Defunct functions in package 'minfi'

minfi-deprecated: Deprecated functions in package 'minfi'

minfi-package: Analyze Illumina's methylation arrays

minfiQC: easy one-step QC of methylation object

plotBetasByType: Plot the overall distribution of beta values and the...

plotCpg: Plot methylation values at an single genomic position

preprocessFunnorm: Functional normalization for Illumina 450k arrays

preprocessIllumina: Perform preprocessing as Genome Studio.

preprocessNoob: The Noob/ssNoob preprocessing method for Infinium methylation...

preprocessQuantile: Stratified quantile normalization for an Illumina methylation...

preprocessRaw: Creation of a MethylSet without normalization

preprocessSwan: Subset-quantile Within Array Normalisation for Illumina...

qcReport: QC report for Illumina Infinium Human Methylation 450k arrays

ratioConvert-methods: Converting methylation signals to ratios (Beta or M-values)

RatioSet-class: RatioSet instances

readGEORawFile: Read in Unmethylated and Methylated signals from a GEO raw...

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

readTCGA: Read in tab deliminited file in the TCGA format

RGChannelSet-class: Class '"RGChannelSet"'

subsetByLoci: Subset an RGChannelset by CpG loci.

utils: Various utilities

Functions

addQC Man page
addSex Man page
addSnpInfo Man page
annotation,GenomicMethylSet-method Man page
annotation,GenomicRatioSet-method Man page
bgcorrect.illumina Man page
blockFinder Man page
bumphunter,GenomicRatioSet-method Man page
combineArrays Man page
combineArrays,GenomicMethylSet,GenomicMethylSet-method Man page
combineArrays,GenomicRatioSet,GenomicRatioSet-method Man page
combineArrays,MethylSet,MethylSet-method Man page
combineArrays,RatioSet,RatioSet-method Man page
combineArrays,RGChannelSet,RGChannelSet-method Man page
combine,GenomicMethylSet,GenomicMethylSet-method Man page
combine,GenomicRatioSet,GenomicRatioSet-method Man page
combine,MethylSet,MethylSet-method Man page
combine,RatioSet,RatioSet-method Man page
combine,RGChannelSet,RGChannelSet-method Man page
compartments Man page
controlStripPlot Man page
convertArray Man page
convertArray,GenomicMethylSet-method Man page
convertArray,GenomicRatioSet-method Man page
convertArray,MethylSet-method Man page
convertArray,RatioSet-method Man page
convertArray,RGChannelSet-method Man page
cpgCollapse Man page
createCorMatrix Man page
densityBeanPlot Man page
densityPlot Man page
detectionP Man page
dmpFinder Man page
dropLociWithSnps Man page
dropMethylationLoci Man page
estimateCellCounts Man page
extractAB Man page
featureNames,GenomicMethylSet-method Man page
featureNames,GenomicRatioSet-method Man page
fixMethOutliers Man page
gaphunter Man page
GenomicMethylSet Man page
GenomicMethylSet-class Man page
GenomicRatioSet Man page
GenomicRatioSet-class Man page
getAnnotation Man page
getAnnotationObject Man page
getBeta Man page
getBeta,GenomicMethylSet-method Man page
getBeta,GenomicRatioSet-method Man page
getBeta,MethylSet-method Man page
getBeta,RatioSet-method Man page
getBeta,RGChannelSet-method Man page
getCN Man page
getCN,GenomicMethylSet-method Man page
getCN,GenomicRatioSet-method Man page
getCN,MethylSet-method Man page
getCN,RatioSet-method Man page
getControlAddress Man page
getControlTypes Man page
getGenomicRatioSetFromGEO Man page
getGreen Man page
getIslandStatus Man page
getLocations Man page
getM Man page
getManifest Man page
getManifest,character-method Man page
getManifest,IlluminaMethylationAnnotation-method Man page
getManifest,IlluminaMethylationManifest-method Man page
getManifestInfo Man page
getManifest,MethylSet-method Man page
getManifest,RGChannelSet-method Man page
getMeth Man page
getMeth,GenomicMethylSet-method Man page
getMeth,MethylSet-method Man page
getMethSignal Man page
getM,GenomicMethylSet-method Man page
getM,GenomicRatioSet-method Man page
getM,MethylSet-method Man page
getM,RatioSet-method Man page
getOOB Man page
getProbeInfo Man page
getProbeType Man page
getQC Man page
getRed Man page
getSex Man page
getSnpBeta Man page
getSnpInfo Man page
getUnmeth Man page
getUnmeth,GenomicMethylSet-method Man page
getUnmeth,MethylSet-method Man page
IlluminaMethylationAnnotation Man page
IlluminaMethylationAnnotation-class Man page
IlluminaMethylationManifest Man page
IlluminaMethylationManifest-class Man page
ilogit2 Man page
initialize,MethylSet-method Man page
initialize,RatioSet-method Man page
initialize,RGChannelSetExtended-method Man page
initialize,RGChannelSet-method Man page
logit2 Man page
makeGenomicRatioSetFromMatrix Man page
mapToGenome Man page
mapToGenome,GenomicMethylSet-method Man page
mapToGenome,GenomicRatioSet-method Man page
mapToGenome-methods Man page
mapToGenome,MethylSet-method Man page
mapToGenome,RatioSet-method Man page
mapToGenome,RGChannelSet-method Man page
mdsPlot Man page
MethylSet Man page
MethylSet-class Man page
minfi Man page
minfi-defunct Man page
minfi-deprecated Man page
minfi-package Man page
minfiQC Man page
normalize.illumina.control Man page
pData,GenomicMethylSet-method Man page
pData,GenomicRatioSet-method Man page
plotBetasByType Man page
plotCpg Man page
plotQC Man page
plotSex Man page
preprocessFunnorm Man page
preprocessIllumina Man page
preprocessMethod Man page
preprocessMethod,GenomicMethylSet-method Man page
preprocessMethod,GenomicRatioSet-method Man page
preprocessMethod,MethylSet-method Man page
preprocessMethod,RatioSet-method Man page
preprocessNoob Man page
preprocessQuantile Man page
preprocessRaw Man page
preprocessSWAN Man page
qcReport Man page
ratioConvert Man page
ratioConvert,GenomicMethylSet-method Man page
ratioConvert-methods Man page
ratioConvert,MethylSet-method Man page
RatioSet Man page
RatioSet-class Man page
read.450k Man page
read.450k.exp Man page
read.450k.sheet Man page
readGEORawFile Man page
read.metharray Man page
read.metharray.exp Man page
read.metharray.sheet Man page
readTCGA Man page
RGChannelSet Man page
RGChannelSet-class Man page
RGChannelSetExtended Man page
RGChannelSetExtended-class Man page
sampleNames,GenomicMethylSet-method Man page
sampleNames,GenomicRatioSet-method Man page
show,GenomicMethylSet-method Man page
show,GenomicRatioSet-method Man page
show,IlluminaMethylationAnnotation-method Man page
show,IlluminaMethylationManifest-method Man page
show,MethylSet-method Man page
show,RatioSet-method Man page
show,RGChannelSet-method Man page
subsetByLoci Man page

Files

minfi/DESCRIPTION
minfi/NAMESPACE
minfi/R
minfi/R/anno.R minfi/R/blocks.R minfi/R/bumphunter.R minfi/R/combineArrays.R minfi/R/compartments.R minfi/R/dmr.R minfi/R/estimateCellCounts.R minfi/R/gaphunter.R minfi/R/generics.R minfi/R/getSex.R minfi/R/gmset.R minfi/R/grset.R minfi/R/manifest.R minfi/R/minfiQC.R minfi/R/mset.R minfi/R/plot.R minfi/R/plotBetasByType.R minfi/R/preprocess.R minfi/R/preprocessFunnorm.R minfi/R/preprocessNoob.R minfi/R/preprocessQuantile.R minfi/R/preprocessSwan.R minfi/R/qc.R minfi/R/read.450k.R minfi/R/read.geo.R minfi/R/read.manifest.R minfi/R/read.meth.R minfi/R/rgset.R minfi/R/rset.R minfi/R/utils.R
minfi/README.md
minfi/build
minfi/build/vignette.rds
minfi/inst
minfi/inst/CITATION
minfi/inst/NEWS.Rd
minfi/inst/doc
minfi/inst/doc/minfi.R
minfi/inst/doc/minfi.Rmd
minfi/inst/doc/minfi.pdf
minfi/inst/scripts
minfi/inst/scripts/GenomeStudio.R
minfi/inst/testData
minfi/inst/testData/testData_compartments.R
minfi/inst/testData/testData_compartments.Rout
minfi/inst/testData/testData_preprocessFunnorm.R
minfi/inst/testData/testData_preprocessFunnorm.Rout
minfi/inst/testData/testData_preprocessIllumina.R
minfi/inst/testData/testData_preprocessIllumina.Rout
minfi/inst/testData/testData_preprocessNoob.R
minfi/inst/testData/testData_preprocessNoob.Rout
minfi/inst/testData/testData_preprocessQuantile.R
minfi/inst/testData/testData_preprocessQuantile.Rout
minfi/inst/testData/testData_preprocessRaw.R
minfi/inst/testData/testData_preprocessRaw.Rout
minfi/inst/testData/testData_preprocessSWAN.R
minfi/inst/testData/testData_preprocessSWAN.Rout
minfi/inst/unitTests
minfi/inst/unitTests/digest_compartments.rda
minfi/inst/unitTests/digest_preprocessFunnorm.rda
minfi/inst/unitTests/digest_preprocessIllumina.rda
minfi/inst/unitTests/digest_preprocessNoob.rda
minfi/inst/unitTests/digest_preprocessQuantile.rda
minfi/inst/unitTests/digest_preprocessRaw.rda
minfi/inst/unitTests/digest_preprocessSWAN.rda
minfi/inst/unitTests/test_base.R
minfi/inst/unitTests/test_compartments.R
minfi/inst/unitTests/test_preprocess.R
minfi/inst/unitTests/test_qc.R
minfi/man
minfi/man/GenomicMethylSet-class.Rd minfi/man/GenomicRatioSet-class.Rd minfi/man/IlluminaMethylationAnnotation-class.Rd minfi/man/IlluminaMethylationManifest-class.Rd minfi/man/MethylSet-class.Rd minfi/man/RGChannelSet-class.Rd minfi/man/RatioSet-class.Rd minfi/man/blockFinder.Rd minfi/man/bumphunter.Rd minfi/man/combineArrays.Rd minfi/man/compartments.Rd minfi/man/controlStripPlot.Rd minfi/man/convertArray.Rd minfi/man/cpgCollapse.Rd minfi/man/densityBeanPlot.Rd minfi/man/densityPlot.Rd minfi/man/detectionP.Rd minfi/man/dmpFinder.Rd minfi/man/estimateCellCounts.Rd minfi/man/fixMethOutliers.Rd minfi/man/gaphunter.Rd minfi/man/getAnnotation.Rd minfi/man/getGenomicRatioSetFromGEO.Rd minfi/man/getQC.Rd minfi/man/getSex.Rd minfi/man/logit2.Rd minfi/man/makeGenomicRatioSetFromMatrix.Rd minfi/man/mapToGenome-methods.Rd minfi/man/mdsPlot.Rd minfi/man/minfi-defunct.Rd minfi/man/minfi-deprecated.Rd minfi/man/minfi-package.Rd minfi/man/minfiQC.Rd minfi/man/plotBetasByType.Rd minfi/man/plotCpg.Rd minfi/man/preprocessFunnorm.Rd minfi/man/preprocessIllumina.Rd minfi/man/preprocessNoob.Rd minfi/man/preprocessQuantile.Rd minfi/man/preprocessRaw.Rd minfi/man/preprocessSwan.Rd minfi/man/qcReport.Rd minfi/man/ratioConvert-methods.Rd minfi/man/read.metharray.Rd minfi/man/read.metharray.exp.Rd minfi/man/read.metharray.sheet.Rd minfi/man/readGEORawFile.Rd minfi/man/readTCGA.Rd minfi/man/subsetByLoci.Rd minfi/man/utils.Rd
minfi/tests
minfi/tests/runTests.R
minfi/vignettes
minfi/vignettes/minfi.Rmd
minfi/vignettes/minfi.bib
minfi/vignettes/minfiClasses.pdf
minfi/vignettes/minfi_old.Rnw_
minfi/vignettes/minfi_tmp.Rnw_
minfi/vignettes/unsrturl.bst

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