R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 29 found.
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AnalysisRegionResults (Package: MEAL) : AnalysisRegionResults instances

AnalysisResults heir with the analyses performed in a range of the whole genome.

● Data Source: BioConductor
● Keywords:
● Alias: AnalysisRegionResults, AnalysisRegionResults-class, AnalysisRegionResults-methods, RDAPval, RDAPval,AnalysisRegionResults-method, getRDA, getRDA,AnalysisRegionResults-method, getRange, getRange,AnalysisRegionResults-method, globalPval, globalPval,AnalysisRegionResults-method, globalR2, globalR2,AnalysisRegionResults-method, plotRDA,AnalysisRegionResults-method, plotRegionR2,AnalysisRegionResults-method, regionLM, regionLM,AnalysisRegionResults-method, regionR2, regionR2,AnalysisRegionResults-method, snps, snps,AnalysisRegionResults-method, snpsPvals, snpsPvals,AnalysisRegionResults-method, snpsVar, snpsVar,AnalysisRegionResults-method, topRDAhits,AnalysisRegionResults-method
● 0 images

AnalysisResults (Package: MEAL) : AnalysisResults instances

Container with the results of per probe and per region analyses.

● Data Source: BioConductor
● Keywords:
● Alias: AnalysisResults, AnalysisResults-class, AnalysisResults-methods, blocks, blocks,AnalysisResults-method, bumps, bumps,AnalysisResults-method, covariableNames, covariableNames,AnalysisResults-method, dmrCate, dmrCate,AnalysisResults-method, exportResults,AnalysisResults-method, feats, feats,AnalysisResults-method, featvals, featvals,AnalysisResults-method, getGeneVals,AnalysisResults-method, getMs,AnalysisResults-method, model, model,AnalysisResults-method, modelVariables, modelVariables,AnalysisResults-method, pData,AnalysisResults-method, pData<-,AnalysisResults,ANY-method, phenoData,AnalysisResults-method, phenoData<-,AnalysisResults,ANY-method, plotEWAS,AnalysisResults-method, plotQQ,AnalysisResults-method, plotRegion,AnalysisResults-method, plotVolcano,AnalysisResults-method, probeResults, probeResults,AnalysisResults-method, regionResults, regionResults,AnalysisResults-method, sampleNames,AnalysisResults-method, variableNames, variableNames,AnalysisResults-method
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DAPipeline (Package: MEAL) : Perform differential methylation analysis

Wrapper for analysing differential methylation and expression at region and probe level.

● Data Source: BioConductor
● Keywords:
● Alias: DAPipeline
● 0 images

DAProbe (Package: MEAL) : Perform per probe analysis

Compute statistics (t estimate and p-value) for methylation or expression data using linear or robust linear regression.

● Data Source: BioConductor
● Keywords:
● Alias: DAProbe
● 0 images

DARegion (Package: MEAL) : Detect regions differentially methylated

This function is a wrapper of two known region differentially methylated detection methods: Bumphunter and DMRcate. blockFinder implementation present in minfi package is also available.

● Data Source: BioConductor
● Keywords:
● Alias: DARegion
● 0 images

DARegionAnalysis (Package: MEAL) : Analyse methylation or expression in a specific range

Methylation analysis in a genomic range, taking into account snps.

● Data Source: BioConductor
● Keywords:
● Alias: DARegionAnalysis
● 0 images

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

MEAL has three different categories of important functions: processing, analysing and plotting.

● Data Source: BioConductor
● Keywords:
● Alias: MEAL, MEAL-package
● 0 images

RDAset (Package: MEAL) : Calculate RDA for a set

Perform RDA calculation for a AnalysisRegionResults. Feature values will be considered the matrix X and phenotypes the matrix Y. Adjusting for covariates is done using covariable_names stored in the object.

● Data Source: BioConductor
● Keywords:
● Alias: RDAset
● 0 images

calculateRelevantSNPs (Package: MEAL) : Calculate the SNPs correlated to cpgs

This function estimates the correlation between the snps and the cpgs. For each pair cpg-SNP the p-value is returned.

● Data Source: BioConductor
● Keywords:
● Alias: calculateRelevantSNPs
● 0 images

computeRDAR2 (Package: MEAL) : Compute signification of RDA test

Compare R2 obtained in our region of interest with the global R^2 and the R^2 of regions with the same number of probes.

● Data Source: BioConductor
● Keywords:
● Alias: computeRDAR2
● 0 images