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

Files in this package

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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All documentation is copyright its authors; we didn't write any of that.