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.
|Author||Carlos Ruiz [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonz<c3><a1>lez [aut]|
|Date of publication||None|
|Maintainer||Carlos Ruiz <firstname.lastname@example.org>|
AnalysisRegionResults-class: AnalysisRegionResults instances
AnalysisResults-class: AnalysisResults instances
calculateRelevantSNPs: Calculate the SNPs correlated to cpgs
computeRDAR2: Compute signification of RDA test
correlationMethExprs: Computes the correlation between methylation and expression
createRanges: Create 'GenomicRanges' from data.frame
DAPipeline: Perform differential methylation analysis
DAProbe: Perform per probe analysis
DARegion: Detect regions differentially methylated
DARegionAnalysis: Analyse methylation or expression in a specific range
explainedVariance: Calculate R2 for different variables
exportResults-methods: Exports results data.frames to csv files.
filterSet-methods: Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet'
getGeneVals-methods: Get all probes related to gene
MEAL: MEAL (Methylation and Expression AnaLizer): Package for...
MEAL-defunct: Defunct functions
normalSNP: Normalize SNPs values
plotBestFeatures: Plot best n cpgs
plotEWAS-methods: Plot a Manhattan plot with the probe results
plotFeature: Plot values of a feature
plotLM: Plot a vector of R2
plotQQ-methods: QQ plot of probe analysis
plotRDA-methods: Plot RDA results
plotRegion-methods: Plot of the region
plotRegionR2-methods: Plot R2 region values
plotVolcano-methods: Make a Volcano plot with the probe results
preparePhenotype: Process a table of phenotypes
RDAset: Calculate RDA for a set
topRDAhits-methods: Get the top features associated with the RDA