minfi: Analyze Illumina Infinium DNA methylation arrays

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Tools to analyze & visualize Illumina Infinium methylation arrays.

Author
Kasper 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 publication
None
Maintainer
Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
License
Artistic-2.0
Version
1.20.0
URLs

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