Perform methylation analysis


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Documentation for package ‘MEAL’ version 1.0.3

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A B C D E F G M N P R S V misc

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

-- A --

add.genexp Method to add a slot of expression to 'MultiDataSet'.
add.genexp-method Class 'MultiDataSet'
add.methy Method to add a slot of methylation to 'MultiDataSet'.
add.methy-method Class 'MultiDataSet'
add.methy-methods Method to add a slot of methylation to 'MultiDataSet'.
add.set Method to add a slot to 'MultiDataSet'.
add.set-method Class 'MultiDataSet'
add.set-methods Method to add a slot to 'MultiDataSet'.
add.snps Method to add a slot of SNPs to 'MultiDataSet'.
add.snps-method Class 'MultiDataSet'
AnalysisRegionResults AnalysisRegionResults instances
analysisRegionResults AnalysisRegionResults instances
AnalysisRegionResults-class AnalysisRegionResults instances
AnalysisRegionResults-methods AnalysisRegionResults instances
AnalysisResults AnalysisResults instances
analysisResults AnalysisResults instances
AnalysisResults-class AnalysisResults instances
AnalysisResults-methods AnalysisResults instances

-- B --

betas MethylationSet instances
betas-method MethylationSet instances
blocks AnalysisResults instances
blocks-method AnalysisResults instances
bumps AnalysisResults instances
bumps-method AnalysisResults instances

-- C --

calculateRelevantSNPs Calculate the SNPs correlated to cpgs
checkProbes Filter 'MethylationSet' probes
checkProbes-method MethylationSet instances
checkSamples Modify a 'MethylationSet' to only contain common samples
checkSamples-method MethylationSet instances
chrNumToChar Convert chr numbers to chr strings
correlationMethExprs Computes the correlation between methylation and expression
covariableNames AnalysisResults instances
covariableNames-method AnalysisResults instances
createRanges Create 'GenomicRanges' from data.frame

-- D --

DAPipeline Perform differential methylation analysis
DAProbe Perform per probe analysis
DARegion Detect regions differentially methylated
DARegionAnalysis Analyse methylation or expression in a specific range
dmrCate AnalysisResults instances
dmrCate-method AnalysisResults instances

-- E --

explainedVariance Calculate R2 for different variables
exportResults Exports results data.frames to csv files.
exportResults-method AnalysisResults instances

-- F --

feats AnalysisResults instances
feats-method AnalysisResults instances
featvals AnalysisResults instances
featvals-method AnalysisResults instances
filterSet Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet'

-- G --

getGeneVals Get all probes related to gene
getGeneVals-method AnalysisResults instances
getMs Transforms beta values to M-values
getMs-method AnalysisResults instances
getMs-method MethylationSet instances
getRange AnalysisRegionResults instances
getRange-method AnalysisRegionResults instances
getRDA AnalysisRegionResults instances
getRDA-method AnalysisRegionResults instances

-- M --

MEAL MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data
MethylationSet MethylationSet instances
methylationSet MethylationSet instances
MethylationSet-class MethylationSet instances
MethylationSet-methods MethylationSet instances
model AnalysisResults instances
model-method AnalysisResults instances
modelVariables AnalysisResults instances
modelVariables-method AnalysisResults instances
multiCorrMethExprs Computes the correlation between methylation and expression in a genomic range
MultiDataSet-class Class 'MultiDataSet'
MultiDataSet-methods Class 'MultiDataSet'

-- N --

names-method Class 'MultiDataSet'
normalSNP Normalize SNPs values

-- P --

pData-method AnalysisResults instances
pData<--method AnalysisResults instances
phenoData-method AnalysisResults instances
phenoData<--method AnalysisResults instances
plotBestFeatures Plot best n cpgs
plotEWAS Plot a Manhattan plot with the probe results
plotEWAS-method AnalysisResults instances
plotFeature Plot values of a feature
plotQQ QQ plot of probe analysis
plotQQ-method AnalysisResults instances
plotRDA Plot RDA results
plotRDA-method AnalysisRegionResults instances
plotRegion Plot of the region
plotRegion-method AnalysisResults instances
plotRegionR2 Plot R2 region values
plotRegionR2-method AnalysisRegionResults instances
plotVolcano Make a Volcano plot with the probe results
plotVolcano-method AnalysisResults instances
prepareMethylationSet Generating a 'MethylationSet'
preparePhenotype Process a table of phenotypes
probeResults AnalysisResults instances
probeResults-method AnalysisResults instances

-- R --

RDAset Calculate RDA for a set
regionLM AnalysisRegionResults instances
regionLM-method AnalysisRegionResults instances
regionPval AnalysisRegionResults instances
regionPval-method AnalysisRegionResults instances
regionR2 AnalysisRegionResults instances
regionR2-method AnalysisRegionResults instances
regionResults AnalysisResults instances
regionResults-method AnalysisResults instances

-- S --

sampleNames-method AnalysisResults instances
sampleNames-method Class 'MultiDataSet'
snps AnalysisRegionResults instances
snps-method AnalysisRegionResults instances
snpsPvals AnalysisRegionResults instances
snpsPvals-method AnalysisRegionResults instances
snpsVar AnalysisRegionResults instances
snpsVar-method AnalysisRegionResults instances

-- V --

variableNames AnalysisResults instances
variableNames-method AnalysisResults instances

-- misc --

[ Class 'MultiDataSet'
[-method Class 'MultiDataSet'
[[-method Class 'MultiDataSet'