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minfi (version 1.18.2)

Analyze Illumina's methylation arrays

Description

Tools for analyzing and visualizing Illumina's methylation array data.

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Version

Version

1.18.2

License

Artistic-2.0

Issues

122

Pull Requests

7

Stars

59

Forks

73

Maintainer

Kasper Daniel Hansen

Last Published

February 15th, 2017

Functions in minfi (1.18.2)

minfiQC

easy one-step QC of methylation object
read.metharray.sheet

Reading an Illumina methylation sample sheet
RGChannelSet-class

Class "RGChannelSet"
getAnnotation

Accessing annotation for Illumina methylation objects
densityBeanPlot

Density bean plots of methylation Beta values.
mdsPlot

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

Mapping methylation data to the genome
plotCpg

Plot methylation values at an single genomic position
ratioConvert-methods

Converting methylation signals to ratios (Beta or M-values)
preprocessRaw

Creation of a MethylSet without normalization
bumphunter-methods

Methods for function bumphunter in Package minfi
getQC

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

Estimates A/B compartments from Illumina methylation arrays
getSex

Estimating sample sex based on methylation data
preprocessQuantile

Stratified quantile normalization for an Illumina methylation array.
preprocessSWAN

Subset-quantile Within Array Normalisation for Illumina Infinium HumanMethylation450 BeadChips
read.450k.sheet

Reading an Illumina methylation sample sheet
RatioSet-class

RatioSet instances
fixMethOutliers

Fix methylation outliers
read.450k.exp

Reads an entire 450k experiment using a sample sheet
IlluminaMethylationManifest-class

Class "IlluminaMethylationManifest"
cpgCollapse

Collapse methylation values of adjacent CpGs into a summary value.
GenomicMethylSet-class

GenomicMethylSet instances
getGenomicRatioSetFromGEO

Reading Illumina methylation array data from GEO.
preprocessNoob

The Noob background correction for 450k arrays.
read.metharray.exp

Reads an entire metharray experiment using a sample sheet
minfi-package

Analyze Illumina's methylation arrays
qcReport

QC report for Illumina Infinium Human Methylation 450k arrays
blockFinder

Finds blocks of methylation differences for Illumina methylation arrays
preprocessIllumina

Perform preprocessing as Genome Studio.
readTCGA

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

MethylSet instances
estimateCellCounts

Cell Proportion Estimation
getMethSignal

Various utilities
IlluminaMethylationAnnotation-class

Class IlluminaMethylationAnnotation
densityPlot

Density plots of methylation Beta values.
minfi-deprecated

Deprecated functions in package minfi
read.450k

Parsing IDAT files from Illumina methylation arrays.
logit2

logit in base 2.
dmpFinder

Find differentially methylated positions
detectionP

Detection p-values for all probed genomic positions.
preprocessFunnorm

Functional normalization for Illumina 450k arrays
readGEORawFile

Read in Unmethylated and Methylated signals from a GEO raw file.
GenomicRatioSet-class

GenomicRatioSet instances
gaphunter

Find gap signals in 450k data
controlStripPlot

Plot control probe signals.
makeGenomicRatioSetFromMatrix

Make a GenomicRatioSet from a matrix
read.metharray

Parsing IDAT files from Illumina methylation arrays.
plotBetasByType

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