API for perishky/meffil
Efficient algorithms for DNA methylation
| Global functions | |
|---|---|
| .onLoad | Source code |
| EstDimRMT | Source code |
| add.surrogate.variables | Source code |
| adjust.columns | Source code |
| append.gds.columns | Source code |
| applicable.quantile.site.subsets | Source code |
| background.correct | Source code |
| calculate.beta.genotypes | Source code |
| calculate.cnv | Source code |
| calculate.intensity.G | Source code |
| calculate.intensity.R | Source code |
| check.data.frame | Source code |
| check.featureset | Source code |
| check.manifest | Source code |
| check.samplesheet | Source code |
| cnv.features | Source code |
| cnv.predict.sex | Source code |
| cnv.pvalue | Source code |
| collapse.dups | Source code |
| compute.quantiles.target | Source code |
| cpg.plot | Source code |
| create.cell.type.reference | Source code |
| create.cnv.reference | Source code |
| create.gds.matrix | Source code |
| dye.bias.correct | Source code |
| estimate.cell.counts.from.beta | Source code |
| estimate.cell.counts.from.mu | Source code |
| ewas.by.gds | Source code |
| ewas.by.matrix | Source code |
| ewas.limma | Source code |
| ewas.old | Source code |
| ewas.test.glm | Source code |
| ewas.test.models | Source code |
| ewas.test.rlm | Source code |
| exists.rg | Source code |
| extract.beadnum | Source code |
| extract.controls | Source code |
| extract.detection.pvalues | Source code |
| extract.featureset | Source code |
| extract.from.samplesheet | Source code |
| extract.probes | Source code |
| extract.snp.betas | Source code |
| filter.features | Source code |
| filter.sites | Source code |
| format.relationship | Source code |
| get.all.features | Source code |
| get.basenames | Source code |
| get.beta | Source code |
| get.cell.type.reference | Source code |
| get.cnv.reference | Source code |
| get.index.list | Source code |
| get.island.site.subsets | Source code |
| get.quantile.site.subsets | Source code |
| guess.batch.vars | Man page Source code |
| guess.chip | Source code |
| guess.featureset | Source code |
| huber.2 | Source code |
| identify.dups | Source code |
| impute.matrix | Source code |
| is.autosomal | Source code |
| is.cell.count.object | Source code |
| is.cell.type.reference | Source code |
| is.chromosome | Source code |
| is.cnv.reference | Source code |
| is.compatible.chip | Source code |
| is.ewas.object | Source code |
| is.mu | Source code |
| is.normalized.object | Source code |
| is.qc.object | Source code |
| is.rg | Source code |
| is.sex.specific.subset | Source code |
| is.valid.site.subset | Source code |
| isva | Source code |
| isvaFn | Source code |
| knit.report | Source code |
| lapply.gds | Source code |
| lmfit.safer | Source code |
| lmfit.safer.old | Source code |
| load.globals | Source code |
| make.samplename.from.basename | Source code |
| meffil.add.cell.type.reference | Man page Source code |
| meffil.add.chip | Man page Source code |
| meffil.add.cnv.reference | Man page Source code |
| meffil.add.copynumber450k.references | Man page Source code |
| meffil.add.featureset | Man page Source code |
| meffil.all.features | Man page Source code |
| meffil.autosomal.subset | Man page Source code |
| meffil.basenames | Man page Source code |
| meffil.calculate.cnv | Man page Source code |
| meffil.cell.count.estimates | Man page Source code |
| meffil.cell.count.qc.plots | Man page Source code |
| meffil.cell.type.specific.methylation | Man page Source code |
| meffil.cnv.matrix | Man page Source code |
| meffil.collapse.dups | Man page Source code |
| meffil.control.matrix | Man page Source code |
| meffil.create.qc.object | Man page Source code |
| meffil.create.samplesheet | Man page Source code |
| meffil.design.matrix | Man page Source code |
| meffil.estimate.cell.counts | Man page Source code |
| meffil.estimate.cell.counts.from.betas | Man page Source code |
| meffil.ewas | Man page Source code |
| meffil.ewas.bedgraph | Man page Source code |
| meffil.ewas.covariate.associations | Man page Source code |
| meffil.ewas.cpg.plot | Man page Source code |
| meffil.ewas.manhattan.plot | Man page Source code |
| meffil.ewas.old | Man page Source code |
| meffil.ewas.parameters | Man page Source code |
| meffil.ewas.qq.plot | Man page Source code |
| meffil.ewas.report | Man page Source code |
| meffil.ewas.sample.characteristics | Man page Source code |
| meffil.ewas.summary | Man page Source code |
| meffil.extract.genotypes | Man page Source code |
| meffil.featureset | Man page Source code |
| meffil.gds.apply | Man page Source code |
| meffil.gds.detection.pvalues | Man page Source code |
| meffil.gds.dims | Man page Source code |
| meffil.gds.methylation | Man page Source code |
| meffil.get.autosomal.sites | Man page Source code |
| meffil.get.beta | Man page Source code |
| meffil.get.features | Man page Source code |
| meffil.get.sites | Man page Source code |
| meffil.get.typeii.sites | Man page Source code |
| meffil.get.x.sites | Man page Source code |
| meffil.get.y.sites | Man page Source code |
| meffil.handle.outliers | Man page Source code |
| meffil.list.cell.type.references | Man page Source code |
| meffil.list.chips | Man page Source code |
| meffil.list.cnv.references | Man page Source code |
| meffil.list.featuresets | Man page Source code |
| meffil.load.controls | Man page Source code |
| meffil.load.detection.pvalues | Man page Source code |
| meffil.load.raw.data | Man page Source code |
| meffil.methylation.pcs | Man page |
| meffil.most.variable.cpgs | Man page Source code |
| meffil.normalization.parameters | Man page Source code |
| meffil.normalization.parameters.from.betas | Man page Source code |
| meffil.normalization.report | Man page Source code |
| meffil.normalization.report.from.betas | Man page Source code |
| meffil.normalization.summary | Man page Source code |
| meffil.normalization.summary.from.betas | Man page Source code |
| meffil.normalize.dataset | Man page Source code |
| meffil.normalize.quantiles | Man page Source code |
| meffil.normalize.sample | Man page Source code |
| meffil.normalize.samples | Man page Source code |
| meffil.pcs | Man page Source code |
| meffil.plot.beadnum.cpgs | Man page |
| meffil.plot.beadnum.samples | Man page |
| meffil.plot.cell.counts | Man page |
| meffil.plot.control.batch | Man page Source code |
| meffil.plot.control.scree | Man page Source code |
| meffil.plot.controlmeans | Man page |
| meffil.plot.detectionp.cpgs | Man page |
| meffil.plot.detectionp.samples | Man page |
| meffil.plot.genotypes | Man page |
| meffil.plot.meth.unmeth | Man page |
| meffil.plot.pc.fit | Man page Source code |
| meffil.plot.probe.batch | Man page Source code |
| meffil.plot.probe.batch.from.betas | Man page Source code |
| meffil.plot.sex | Man page |
| meffil.probe.info | Man page Source code |
| meffil.qc | Man page Source code |
| meffil.qc.parameters | Man page |
| meffil.qc.report | Man page Source code |
| meffil.qc.summary | Man page Source code |
| meffil.read.samplesheet | Man page Source code |
| meffil.remove.samples | Man page |
| meffil.save.detection.pvalues | Man page Source code |
| meffil.snp.betas | Man page Source code |
| meffil.snp.concordance | Man page Source code |
| meffil.snp.names | Man page Source code |
| meffil.summarize.relationship | Man page Source code |
| msg | Source code |
| mu.to.cn | Source code |
| normalize.quantiles | Source code |
| partition.integer.subsequence | Source code |
| pca.to.design.matrix | Source code |
| plot.pairwise.associations | Source code |
| plot.pcs | Source code |
| plot.pcs.from.betas | Source code |
| qq.lambda | Source code |
| quantile.normalize.betas | Source code |
| quantile.normalize.signals | Source code |
| read.idat | Source code |
| read.rg | Source code |
| retrieve.gds.cpg.sites | Source code |
| retrieve.gds.dims | Source code |
| retrieve.gds.matrix | Source code |
| retrieve.gds.methylation | Source code |
| retrieve.gds.samples | Source code |
| rg.to.mu | Source code |
| save.globals | Source code |
| scatter.thinning | Source code |
| simplify.variable | Source code |
| test.pairwise.associations | Source code |
| visualize.relationship | Source code |
| winsorize | Source code |
