Man pages for Bioconductor-mirror/minfi
Analyze Illumina Infinium DNA methylation arrays

blockFinderFinds blocks of methylation differences for Illumina...
bumphunterMethods for function 'bumphunter' in Package 'minfi'
combineArraysA method for combining different types of methylation arrays...
compartmentsEstimates A/B compartments from Illumina methylation arrays
controlStripPlotPlot control probe signals.
convertArrayA method for converting a type of methylation arrays into a...
cpgCollapseCollapse methylation values of adjacent CpGs into a summary...
densityBeanPlotDensity bean plots of methylation Beta values.
densityPlotDensity plots of methylation Beta values.
detectionPDetection p-values for all probed genomic positions.
dmpFinderFind differentially methylated positions
estimateCellCountsCell Proportion Estimation
fixMethOutliersFix methylation outliers
gaphunterFind gap signals in 450k data
GenomicMethylSet-classGenomicMethylSet instances
GenomicRatioSet-classGenomicRatioSet instances
getAnnotationAccessing annotation for Illumina methylation objects
getGenomicRatioSetFromGEOReading Illumina methylation array data from GEO.
getQCEstimate sample-specific quality control (QC) for methylation...
getSexEstimating sample sex based on methylation data
IlluminaMethylationAnnotation-classClass 'IlluminaMethylationAnnotation'
IlluminaMethylationManifest-classClass '"IlluminaMethylationManifest"'
logit2logit in base 2.
makeGenomicRatioSetFromMatrixMake a GenomicRatioSet from a matrix
mapToGenome-methodsMapping methylation data to the genome
mdsPlotMulti-dimensional scaling plots giving an overview of...
MethylSet-classMethylSet instances
minfi-defunctDefunct functions in package 'minfi'
minfi-deprecatedDeprecated functions in package 'minfi'
minfi-packageAnalyze Illumina's methylation arrays
minfiQCeasy one-step QC of methylation object
plotBetasByTypePlot the overall distribution of beta values and the...
plotCpgPlot methylation values at an single genomic position
preprocessFunnormFunctional normalization for Illumina 450k arrays
preprocessIlluminaPerform preprocessing as Genome Studio.
preprocessNoobThe Noob/ssNoob preprocessing method for Infinium methylation...
preprocessQuantileStratified quantile normalization for an Illumina methylation...
preprocessRawCreation of a MethylSet without normalization
preprocessSwanSubset-quantile Within Array Normalisation for Illumina...
qcReportQC report for Illumina Infinium Human Methylation 450k arrays
ratioConvert-methodsConverting methylation signals to ratios (Beta or M-values)
RatioSet-classRatioSet instances
readGEORawFileRead in Unmethylated and Methylated signals from a GEO raw...
read.metharrayParsing IDAT files from Illumina methylation arrays.
read.metharray.expReads an entire metharray experiment using a sample sheet
read.metharray.sheetReading an Illumina methylation sample sheet
readTCGARead in tab deliminited file in the TCGA format
RGChannelSet-classClass '"RGChannelSet"'
subsetByLociSubset an RGChannelset by CpG loci.
utilsVarious utilities
Bioconductor-mirror/minfi documentation built on July 1, 2017, 7:39 a.m.