Package: minfi 1.59.1

Kasper Daniel Hansen

minfi: Analyze Illumina Infinium DNA methylation arrays

Tools to analyze & visualize Illumina Infinium methylation arrays.

Authors: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], Peter F. Hickey [ctb]

minfi_1.59.1.tar.gz
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minfi_1.59.1.tgz(r-4.6-any)minfi_1.59.1.tgz(r-4.5-any)
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
minfi/json (API)

# Install 'minfi' in R:

install.packages('minfi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hansenlab/minfi/issues

On BioConductor:minfi-1.59.1(bioc 3.24)minfi-1.58.0(bioc 3.23)

immunooncology dnamethylation differentialmethylation epigenetics microarray methylationarray multichannel twochannel dataimport normalization preprocessing qualitycontrol

12.69 score 64 stars 34 packages 2.3k scripts 506 mentions 95 exports 137 dependencies

Last updated from:fa38de7846. Checks:8 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	586
linux-devel-x86_64	WARNING	920
source / vignettes	OK	742
linux-release-x86_64	WARNING	1014
macos-release-arm64	WARNING	482
macos-oldrel-arm64	WARNING	543
windows-devel	WARNING	836
windows-release	WARNING	776
windows-oldrel	WARNING	770
wasm-release	OK	592

Exports:addQC addSex addSnpInfo annotation annotation<-bgcorrect.illumina blockFinder bumphunter coerce combine combineArrays compartments controlStripPlot convertArray cpgCollapse createCorMatrix densityBeanPlot densityPlot detectionP dmpFinder dropLociWithSnps dropMethylationLoci estimateCellCounts extractAB featureNames featureNames<-fixMethOutliers gaphunter GenomicMethylSet GenomicRatioSet getAnnotation getAnnotationObject getBeta getCN getControlAddress getGenomicRatioSetFromGEO getGreen getIslandStatus getLocations getM getManifest getManifestInfo getMeth getMethSignal getNBeads getOOB getProbeInfo getProbeType getQC getRed getSex getSnpBeta getSnpInfo getUnmeth IlluminaMethylationAnnotation IlluminaMethylationManifest ilogit2 initialize logit2 makeGenomicRatioSetFromMatrix mapToGenome mdsPlot MethylSet minfiQC normalize.illumina.control pData pData<-plotBetasByType plotCpg plotQC plotSex preprocessFunnorm preprocessIllumina preprocessMethod preprocessNoob preprocessQuantile preprocessRaw preprocessSWAN qcReport ratioConvert RatioSet read.450k read.450k.exp read.450k.sheet read.metharray read.metharray.exp read.metharray.sheet readGEORawFile readTCGA RGChannelSet RGChannelSetExtended sampleNames sampleNames<-show subsetByLoci

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry doRNG dplyr fastmap filelock foreach formatR futile.logger futile.options genefilter generics GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue h5mread HDF5Array hms httr httr2 illuminaio IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime multtest nlme nor1mix openssl pillar pkgconfig plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scrime selectr Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr XML xml2 xtable XVector yaml

The minfi User's Guide

Rendered fromminfi.Rmdusingknitr::rmarkdown

Last update: 2017-10-16
Started: 2016-03-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Analyze Illumina's methylation arrays	minfi-package minfi
Finds blocks of methylation differences for Illumina methylation arrays	blockFinder
Methods for function 'bumphunter' in Package 'minfi'	bumphunter,GenomicRatioSet-method
A method for combining different types of methylation arrays into a virtual array.	combineArrays combineArrays,GenomicMethylSet,GenomicMethylSet-method combineArrays,GenomicRatioSet,GenomicRatioSet-method combineArrays,MethylSet,MethylSet-method combineArrays,RatioSet,RatioSet-method combineArrays,RGChannelSet,RGChannelSet-method
Estimates A/B compartments from Illumina methylation arrays	compartments createCorMatrix extractAB
Plot control probe signals.	controlStripPlot
A method for converting a type of methylation arrays into a virtual array of another type.	convertArray convertArray,GenomicMethylSet-method convertArray,GenomicRatioSet-method convertArray,MethylSet-method convertArray,RatioSet-method convertArray,RGChannelSet-method
Collapse methylation values of adjacent CpGs into a summary value.	cpgCollapse
Density bean plots of methylation Beta values.	densityBeanPlot
Density plots of methylation Beta values.	densityPlot
Detection p-values for all probed genomic positions.	detectionP
Find differentially methylated positions	dmpFinder
Cell Proportion Estimation	estimateCellCounts
Fix methylation outliers	fixMethOutliers
Find gap signals in 450k data	gaphunter
GenomicMethylSet instances	annotation,GenomicMethylSet-method annotation<-,GenomicMethylSet,ANY-method combine,GenomicMethylSet,GenomicMethylSet-method featureNames,GenomicMethylSet-method featureNames<-,GenomicMethylSet-method GenomicMethylSet GenomicMethylSet-class getBeta,GenomicMethylSet-method getCN,GenomicMethylSet-method getM,GenomicMethylSet-method getMeth,GenomicMethylSet-method getUnmeth,GenomicMethylSet-method mapToGenome,GenomicMethylSet-method pData,GenomicMethylSet-method pData<-,GenomicMethylSet,DataFrame-method preprocessMethod,GenomicMethylSet-method sampleNames,GenomicMethylSet-method sampleNames<-,GenomicMethylSet,ANY-method show,GenomicMethylSet-method
GenomicRatioSet instances	annotation,GenomicRatioSet-method annotation<-,GenomicRatioSet,ANY-method combine,GenomicRatioSet,GenomicRatioSet-method featureNames,GenomicRatioSet-method featureNames<-,GenomicRatioSet-method GenomicRatioSet GenomicRatioSet-class getBeta,GenomicRatioSet-method getCN getCN,GenomicRatioSet-method getM,GenomicRatioSet-method mapToGenome,GenomicRatioSet-method pData,GenomicRatioSet-method pData<-,GenomicRatioSet,DataFrame-method preprocessMethod,GenomicRatioSet-method sampleNames,GenomicRatioSet-method sampleNames<-,GenomicRatioSet,ANY-method show,GenomicRatioSet-method
Accessing annotation for Illumina methylation objects	addSnpInfo dropLociWithSnps getAnnotation getAnnotationObject getIslandStatus getLocations getProbeType getSnpInfo
Reading Illumina methylation array data from GEO.	getGenomicRatioSetFromGEO
Various utilities	getMethSignal
Estimate sample-specific quality control (QC) for methylation data	addQC getQC plotQC
Estimating sample sex based on methylation data	addSex getSex plotSex
Class 'IlluminaMethylationAnnotation'	getManifest,IlluminaMethylationAnnotation-method IlluminaMethylationAnnotation IlluminaMethylationAnnotation-class show,IlluminaMethylationAnnotation-method
Class '"IlluminaMethylationManifest"'	getControlAddress getManifest getManifest,character-method getManifest,IlluminaMethylationManifest-method getManifestInfo getProbeInfo IlluminaMethylationManifest IlluminaMethylationManifest-class show,IlluminaMethylationManifest-method
logit in base 2.	ilogit2 logit2
Make a GenomicRatioSet from a matrix	makeGenomicRatioSetFromMatrix
Mapping methylation data to the genome	mapToGenome mapToGenome,MethylSet-method mapToGenome,RatioSet-method mapToGenome,RGChannelSet-method mapToGenome-methods
Multi-dimensional scaling plots giving an overview of similarities and differences between samples.	mdsPlot
MethylSet instances	annotation,MethylSet-method annotation<-,MethylSet,ANY-method combine,MethylSet,MethylSet-method dropMethylationLoci featureNames,MethylSet-method featureNames<-,MethylSet-method getBeta getBeta,MethylSet-method getCN,MethylSet-method getM getM,MethylSet-method getManifest,MethylSet-method getMeth getMeth,MethylSet-method getUnmeth getUnmeth,MethylSet-method MethylSet MethylSet-class pData,MethylSet-method pData<-,MethylSet,DataFrame-method preprocessMethod preprocessMethod,MethylSet-method sampleNames,MethylSet-method sampleNames<-,MethylSet,ANY-method show,MethylSet-method
Defunct functions in package 'minfi'	minfi-defunct read.450k read.450k.exp read.450k.sheet
Deprecated functions in package 'minfi'	minfi-deprecated
easy one-step QC of methylation object	minfiQC
Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types.	plotBetasByType
Plot methylation values at an single genomic position	plotCpg
Functional normalization for Illumina 450k arrays	preprocessFunnorm
Perform preprocessing as Genome Studio.	bgcorrect.illumina normalize.illumina.control preprocessIllumina
The Noob/ssNoob preprocessing method for Infinium methylation microarrays.	preprocessNoob
Stratified quantile normalization for an Illumina methylation array.	preprocessQuantile
Creation of a MethylSet without normalization	preprocessRaw
Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips	preprocessSWAN
QC report for Illumina Infinium Human Methylation 450k arrays	qcReport
Converting methylation signals to ratios (Beta or M-values)	ratioConvert ratioConvert,GenomicMethylSet-method ratioConvert,MethylSet-method ratioConvert-methods
RatioSet instances	annotation,RatioSet-method annotation<-,RatioSet,ANY-method combine,RatioSet,RatioSet-method featureNames,RatioSet-method featureNames<-,RatioSet-method getBeta,RatioSet-method getCN,RatioSet-method getM,RatioSet-method pData,RatioSet-method pData<-,RatioSet,DataFrame-method preprocessMethod,RatioSet-method RatioSet RatioSet-class sampleNames,RatioSet-method sampleNames<-,RatioSet,ANY-method show,RatioSet-method
Parsing IDAT files from Illumina methylation arrays.	read.metharray
Reads an entire metharray experiment using a sample sheet	read.metharray.exp
Reading an Illumina methylation sample sheet	read.metharray.sheet
Read in Unmethylated and Methylated signals from a GEO raw file.	readGEORawFile
Read in tab deliminited file in the TCGA format	readTCGA
Class '"RGChannelSet"'	annotation,RGChannelSet-method annotation<-,RGChannelSet,ANY-method coerce,RGChannelSetExtended,RGChannelSet-method combine,RGChannelSet,RGChannelSet-method featureNames,RGChannelSet-method featureNames<-,RGChannelSet-method getBeta,RGChannelSet-method getGreen getManifest,RGChannelSet-method getNBeads getOOB getRed getSnpBeta pData,RGChannelSet-method pData<-,RGChannelSet,DataFrame-method RGChannelSet RGChannelSet-class RGChannelSetExtended RGChannelSetExtended-class sampleNames,RGChannelSet-method sampleNames<-,RGChannelSet,ANY-method show,RGChannelSet-method
Subset an RGChannelset by CpG loci.	subsetByLoci