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MEAL (version 1.2.3)

Perform methylation analysis

Description

Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

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Version

Version

1.2.3

License

Artistic-2.0

Maintainer

Carlos Ruiz

Last Published

February 15th, 2017

Functions in MEAL (1.2.3)

AnalysisRegionResults

AnalysisRegionResults instances
calculateRelevantSNPs

Calculate the SNPs correlated to cpgs
computeRDAR2

Compute signification of RDA test
topRDAhits

Get the top features associated with the RDA
DARegionAnalysis

Analyse methylation or expression in a specific range
plotBestFeatures

Plot best n cpgs
DAPipeline

Perform differential methylation analysis
RDAset

Calculate RDA for a set
plotLM

Plot a vector of R2
DARegion

Detect regions differentially methylated
explainedVariance

Calculate R2 for different variables
normalSNP

Normalize SNPs values
plotRDA

Plot RDA results
getGeneVals

Get all probes related to gene
plotRegionR2

Plot R2 region values
multiCorrMethExprs

Computes the correlation between methylation and expression in a genomic range
MEAL

MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data
plotVolcano

Make a Volcano plot with the probe results
plotRegion

Plot of the region
plotEWAS

Plot a Manhattan plot with the probe results
createRanges

Create GenomicRanges from data.frame
DAProbe

Perform per probe analysis
correlationMethExprs

Computes the correlation between methylation and expression
AnalysisResults

AnalysisResults instances
plotFeature

Plot values of a feature
plotQQ

QQ plot of probe analysis
filterSet

Filter a MethylationSet, an ExpressionSet or a SnpSet
exportResults

Exports results data.frames to csv files.
preparePhenotype

Process a table of phenotypes