Man pages for perishky/meffil
Efficient algorithms for DNA methylation

guess.batch.varsGuess which columns in sample sheet are batch variables
meffil.add.cell.type.referenceCreate a cell type reference object
meffil.add.chipAdd a new chip for analysis.
meffil.add.cnv.referenceCreate a copy number reference object
meffil.add.copynumber450k.referencesCreate copy number references from CopyNumber450kData
meffil.add.featuresetAdd a feature set.
meffil.basenamesIDAT file basenames
meffil.calculate.cnvCalculate CNVs from IDAT files
meffil.cell.count.estimatesCell count estimates
meffil.cell.count.qc.plotsCell count estimate quality plot
meffil.cell.type.specific.methylationReduce methylation profiles to most cell-type specific sites
meffil.cnv.matrixCreate matrix of CNV values
meffil.control.matrixInfinium HumanMethylation450 BeadChip control matrix
meffil.create.qc.objectQuality control object
meffil.create.samplesheetCreate sample sheet if an Illumina one isn't available HumanMethylation450 BeadChip normalization design...
meffil.estimate.cell.countsEstimate cell counts from a reference
meffil.estimate.cell.counts.from.betasEstimate cell counts for a beta matrix from a reference
meffil.ewasEpigenome-wide association study
meffil.ewas.covariate.associationsDescribe associations between EWAS covariates and the...
meffil.ewas.cpg.plotScatter plots for a CpG site in an EWAS
meffil.ewas.manhattan.plotManhattan plot for EWAS
meffil.ewas.parametersSpecify parameters for QC
meffil.ewas.qq.plotQQ plot for EWAS
meffil.ewas.reportGenerate EWAS report.
meffil.ewas.sample.characteristicsDescribe EWAS samples using the variable of interest and...
meffil.ewas.summarySummarize EWAS results.
meffil.extract.genotypesExtract genotype data from PLINK .raw files for Illumina 450K...
meffil.featuresetObtain a list of features in a feature set.
meffil.get.autosomal.sitesGet names of autosomal CpG sites in the feature set.
meffil.get.betaInfinium HumanMethylation450 BeadChip methylation levels
meffil.get.featuresGet a list of microarray features from a predefined feature...
meffil.get.sitesGet names of all CpG sites in the feature set.
meffil.get.typeii.sitesGet names of CpG sites corresponding to Infinium Type II...
meffil.get.x.sitesGet names of chromosome X CpG sites in the feature set.
meffil.get.y.sitesGet names of chromosome Y CpG sites in the feature set.
meffil.list.cell.type.referencesList of available cell type references
meffil.list.chipsList of microarrays formats available.
meffil.list.cnv.referencesList of available copy number references
meffil.list.featuresetsList of feature sets available.
meffil.load.controlsLoad control probes
meffil.load.detection.pvaluesLoad detection p-value matrix
meffil.load.raw.dataLoad raw beta matrix
meffil.methylation.pcsCompute principal components of a methylation matrix.
meffil.most.variable.cpgsMost variable CpG sites
meffil.normalization.parametersSpecify parameters for testing normalization
meffil.normalization.reportGenerate report on normalization performance
meffil.normalization.summaryPerform tests to check normalization performance
meffil.normalize.datasetFunctional normalization
meffil.normalize.quantilesNormalize microarray quantiles
meffil.normalize.sampleNormalize Infinium HumanMethylation450 BeadChip
meffil.normalize.samplesNormalize Infinium HumanMethylation450 BeadChips
meffil.pcsCalculate control probe PCs
meffil.plot.beadnum.cpgsManhattan plot of number of beads by probe - percentage of...
meffil.plot.beadnum.samplesPlot number of beads per sample
meffil.plot.cell.countsCell count estimate quality plot
meffil.plot.control.batchTest for association of control matrix probes with known...
meffil.plot.controlmeansPlot the means of control probes for each sample and for each...
meffil.plot.control.screePlot scree plot of control matrix
meffil.plot.detectionp.cpgsManhattan plot of detection pval per probe - percentage with...
meffil.plot.detectionp.samplesPlot detection p values from idat files
meffil.plot.genotypesPlot SNP beta and sample genotype concordances
meffil.plot.meth.unmethPlot average methylated vs unmethylated levels for each...
meffil.plot.pc.fitNumber of control matrix principal components
meffil.plot.probe.batchTest normalized betas for association with known batch...
meffil.plot.sexPlot predicted sex
meffil.probe.infoObtain a list of probes for a given feature set (chip).
meffil.qcPerform QC on HumanMethylation450 idat files
meffil.qc.parametersSpecify parameters for QC
meffil.qc.reportGenerate QC report
meffil.qc.summaryPerform QC analysis on idat files to read Illumina "Sample Sheet" adapted from...
meffil.remove.samplesRemove samples from QC objects
meffil.snp.betasMatrix of SNP 'beta' values
meffil.snp.concordanceConcordance between genotypes and SNP betas
meffil.snp.namesObtain the list of identifiers for the SNPs on the...
meffil.summarize.relationshipDescribe the relationship between two variables.
perishky/meffil documentation built on Dec. 3, 2019, 2:05 a.m.