Files in minfi

Analyze Illumina Infinium DNA methylation arrays

README.md R/preprocessRaw.R R/DelayedArray_utils.R R/read.manifest.R R/dmpFinder.R R/RatioSet-class.R R/plotBetasByType.R R/qc.R R/preprocessQuantile.R R/eSet_methods.R R/read.geo.R R/GenomicMethylSet-class.R R/IlluminaMethylationManifest-class.R R/IlluminaMethylationAnnotation-class.R R/AllGenerics.R R/estimateCellCounts.R R/preprocessFunnorm.R R/utils.R R/detectionP.R R/preprocessIllumina.R R/RGChannelSetExtended-class.R R/read.meth2.R R/bumphunter.R R/preprocessNoob.R R/plot.R R/RGChannelSet-class.R R/getSex.R R/read.meth.R R/compartments.R R/blocks.R R/minfiQC.R R/preprocessSwan.R R/GenomicRatioSet-class.R R/read.450k.R R/MethylSet-class.R R/gaphunter.R R/combineArrays.R vignettes/minfiClasses.pdf vignettes/minfi.Rmd man/GenomicRatioSet-class.Rd man/preprocessIllumina.Rd man/getSex.Rd man/estimateCellCounts.Rd man/getQC.Rd man/RatioSet-class.Rd man/qcReport.Rd man/GenomicMethylSet-class.Rd man/dmpFinder.Rd man/read.metharray.exp.Rd man/getGenomicRatioSetFromGEO.Rd man/DelayedArray_utils.Rd man/getAnnotation.Rd man/detectionP.Rd man/mdsPlot.Rd man/RGChannelSet-class.Rd man/minfiQC.Rd man/mapToGenome-methods.Rd man/blockFinder.Rd man/minfi-package.Rd man/cpgCollapse.Rd man/subsetByLoci.Rd man/MethylSet-class.Rd man/readGEORawFile.Rd man/plotCpg.Rd man/fixMethOutliers.Rd man/preprocessQuantile.Rd man/logit2.Rd man/preprocessRaw.Rd man/bumphunter.Rd man/makeGenomicRatioSetFromMatrix.Rd man/preprocessFunnorm.Rd man/densityPlot.Rd man/controlStripPlot.Rd man/preprocessSwan.Rd man/utils.Rd man/gaphunter.Rd man/densityBeanPlot.Rd man/minfi-deprecated.Rd man/compartments.Rd man/plotBetasByType.Rd man/read.metharray.Rd man/convertArray.Rd man/minfi-defunct.Rd man/readTCGA.Rd man/IlluminaMethylationManifest-class.Rd man/IlluminaMethylationAnnotation-class.Rd man/preprocessNoob.Rd man/ratioConvert-methods.Rd man/read.metharray.sheet.Rd man/combineArrays.Rd tests/runTests.R inst/doc/minfi.R inst/doc/minfi.Rmd inst/scripts/GenomeStudio.R inst/testData/testData_preprocessQuantile.R inst/testData/testData_compartments.R inst/testData/testData_preprocessFunnorm.R inst/testData/testData_preprocessIllumina.R inst/testData/testData_preprocessRaw.R inst/testData/testData_preprocessSWAN.R inst/testData/testData_preprocessNoob.R inst/unitTests/test_examples_with_DelayedArray.R inst/unitTests/test_qc.R inst/unitTests/test_compartments.R inst/unitTests/test_base.R inst/unitTests/test_preprocess.R