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 |
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 |
betas | MethylationSet instances |
betas-method | MethylationSet instances |
blocks | AnalysisResults instances |
blocks-method | AnalysisResults instances |
bumps | AnalysisResults instances |
bumps-method | AnalysisResults instances |
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 |
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 |
explainedVariance | Calculate R2 for different variables |
exportResults | Exports results data.frames to csv files. |
exportResults-method | AnalysisResults instances |
feats | AnalysisResults instances |
feats-method | AnalysisResults instances |
featvals | AnalysisResults instances |
featvals-method | AnalysisResults instances |
filterSet | Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet' |
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 |
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' |
names-method | Class 'MultiDataSet' |
normalSNP | Normalize SNPs values |
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 |
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 |
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 |
variableNames | AnalysisResults instances |
variableNames-method | AnalysisResults instances |
[ | Class 'MultiDataSet' |
[-method | Class 'MultiDataSet' |
[[-method | Class 'MultiDataSet' |