Files in minfi

Analyze Illumina Infinium DNA methylation arrays

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

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/minfi_tmp.Rnw_

vignettes/minfiClasses.pdf

vignettes/unsrturl.bst

vignettes/minfi_old.Rnw_

vignettes/minfi.bib

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/NEWS.Rd

inst/CITATION

inst/doc/minfi.R

inst/doc/minfi.html

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.Rout

inst/testData/testData_compartments.Rout

inst/testData/testData_preprocessFunnorm.Rout

inst/testData/testData_preprocessIllumina.R inst/testData/testData_preprocessRaw.R

inst/testData/testData_preprocessSWAN.Rout

inst/testData/testData_preprocessNoob.Rout

inst/testData/testData_preprocessRaw.Rout

inst/testData/testData_preprocessSWAN.R

inst/testData/testData_preprocessQuantile.Rout

inst/testData/testData_preprocessNoob.R

inst/unitTests/digest_preprocessFunnorm.rda

inst/unitTests/digest_preprocessNoob.rda

inst/unitTests/digest_compartments.rda

inst/unitTests/digest_preprocessIllumina.rda

inst/unitTests/test_examples_with_DelayedArray.R inst/unitTests/test_qc.R

inst/unitTests/digest_preprocessSWAN.rda

inst/unitTests/digest_preprocessQuantile.rda

inst/unitTests/test_compartments.R inst/unitTests/test_base.R inst/unitTests/test_preprocess.R

inst/unitTests/digest_preprocessRaw.rda

minfi documentation built on Nov. 8, 2020, 4:53 p.m.