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R package: minfi

This is the developer version of Bioconductor package minfi. Install in R as:

source('http://bioconductor.org/biocLite.R')
biocLite('minfi')

Software status

Resource:BioconductorTravis CI
Platforms:MultipleLinux
R CMD check (release) (devel)
Test coverage

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Version

Version

1.18.4

License

Artistic-2.0

Issues

124

Pull Requests

8

Stars

64

Forks

74

Maintainer

Kasper Daniel Hansen

Last Published

February 15th, 2017

Functions in minfi (1.18.4)

dmpFinder

Find differentially methylated positions
estimateCellCounts

Cell Proportion Estimation
plotBetasByType

Plot the overall distribution of beta values and the distributions of the Infinium I and II probe types.
plotCpg

Plot methylation values at an single genomic position
preprocessRaw

Creation of a MethylSet without normalization
preprocessSWAN

Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
densityPlot

Density plots of methylation Beta values.
detectionP

Detection p-values for all probed genomic positions.
getAnnotation

Accessing annotation for Illumina methylation objects
getGenomicRatioSetFromGEO

Reading Illumina methylation array data from GEO.
minfi-package

Analyze Illumina's methylation arrays
minfiQC

easy one-step QC of methylation object
RatioSet-class

RatioSet instances
read.450k.exp

Reads an entire 450k experiment using a sample sheet
getMethSignal

Various utilities
GenomicMethylSet-class

GenomicMethylSet instances
GenomicRatioSet-class

GenomicRatioSet instances
makeGenomicRatioSetFromMatrix

Make a GenomicRatioSet from a matrix
logit2

logit in base 2.
read.450k

Parsing IDAT files from Illumina methylation arrays.
read.450k.sheet

Reading an Illumina methylation sample sheet
blockFinder

Finds blocks of methylation differences for Illumina methylation arrays
bumphunter-methods

Methods for function bumphunter in Package minfi
getQC

Estimate sample-specific quality control (QC) for methylation data
qcReport

QC report for Illumina Infinium Human Methylation 450k arrays
getSex

Estimating sample sex based on methylation data
ratioConvert-methods

Converting methylation signals to ratios (Beta or M-values)
read.metharray.sheet

Reading an Illumina methylation sample sheet
readGEORawFile

Read in Unmethylated and Methylated signals from a GEO raw file.
compartments

Estimates A/B compartments from Illumina methylation arrays
controlStripPlot

Plot control probe signals.
IlluminaMethylationAnnotation-class

Class IlluminaMethylationAnnotation
MethylSet-class

MethylSet instances
IlluminaMethylationManifest-class

Class "IlluminaMethylationManifest"
minfi-deprecated

Deprecated functions in package ‘minfi’
preprocessNoob

The Noob background correction for 450k arrays.
readTCGA

Read in tab deliminited file in the TCGA format
RGChannelSet-class

Class "RGChannelSet"
preprocessQuantile

Stratified quantile normalization for an Illumina methylation array.
cpgCollapse

Collapse methylation values of adjacent CpGs into a summary value.
densityBeanPlot

Density bean plots of methylation Beta values.
gaphunter

Find gap signals in 450k data
fixMethOutliers

Fix methylation outliers
mapToGenome-methods

Mapping methylation data to the genome
mdsPlot

Multi-dimensional scaling plots giving an overview of similarities and differences between samples.
preprocessFunnorm

Functional normalization for Illumina 450k arrays
preprocessIllumina

Perform preprocessing as Genome Studio.
read.metharray.exp

Reads an entire metharray experiment using a sample sheet
read.metharray

Parsing IDAT files from Illumina methylation arrays.