Man pages for perishky/meffil
Efficient algorithms for DNA methylation
| guess.batch.vars | Guess which columns in sample sheet are batch variables |
| meffil.add.cell.type.reference | Create a cell type reference object |
| meffil.add.chip | Add a new chip for analysis. |
| meffil.add.cnv.reference | Create a copy number reference object |
| meffil.add.copynumber450k.references | Create copy number references from CopyNumber450kData |
| meffil.add.featureset | Add a feature set. |
| meffil.all.features | Feature information for all Illumina Beadchips |
| meffil.autosomal.subset | Restrict to subset of features targetting autosomal CpG sites |
| meffil.basenames | IDAT file basenames |
| meffil.calculate.cnv | Calculate CNVs from IDAT files |
| meffil.cell.count.estimates | Cell count estimates |
| meffil.cell.count.qc.plots | Cell count estimate quality plot |
| meffil.cell.type.specific.methylation | Reduce methylation profiles to most cell-type specific sites |
| meffil.cnv.matrix | Create matrix of CNV values |
| meffil.collapse.dups | Collapse duplicate probes |
| meffil.control.matrix | Infinium HumanMethylation450 BeadChip control matrix |
| meffil.create.qc.object | Quality control object |
| meffil.create.samplesheet | Create sample sheet if an Illumina one isn't available |
| meffil.design.matrix | Infinium HumanMethylation450 BeadChip normalization design... |
| meffil.estimate.cell.counts | Estimate cell counts from a reference |
| meffil.estimate.cell.counts.from.betas | Estimate cell counts for a methylation matrix from a... |
| meffil.ewas | Epigenome-wide association study |
| meffil.ewas.bedgraph | Save EWAS effect estimates to bedgraph file |
| meffil.ewas.covariate.associations | Describe associations between EWAS covariates and the... |
| meffil.ewas.cpg.plot | Scatter plots for a CpG site in an EWAS |
| meffil.ewas.manhattan.plot | Manhattan plot for EWAS |
| meffil.ewas.old | Epigenome-wide association study (OLD VERSION RETAINED FOR... |
| meffil.ewas.parameters | Specify parameters for QC |
| meffil.ewas.qq.plot | QQ plot for EWAS |
| meffil.ewas.report | Generate EWAS report. |
| meffil.ewas.sample.characteristics | Describe EWAS samples using the variable of interest and... |
| meffil.ewas.summary | Summarize EWAS results. |
| meffil.extract.genotypes | Extract genotype data from PLINK .raw files for Illumina 450K... |
| meffil.featureset | Obtain a list of features in a feature set. |
| meffil.gds.apply | Return a vector or list of values obtained by applying a... |
| meffil.gds.detection.pvalues | Retrieve detection p-values from GDS file |
| meffil.gds.dims | Retrieve methylation or detection p-value matrix row and... |
| meffil.gds.methylation | Retrieve methylation levels from GDS file |
| meffil.get.autosomal.sites | Get names of autosomal CpG sites in the feature set. |
| meffil.get.beta | Infinium HumanMethylation450 BeadChip methylation levels |
| meffil.get.features | Get a list of microarray features from a predefined feature... |
| meffil.get.sites | Get names of all CpG sites in the feature set. |
| meffil.get.typeii.sites | Get names of CpG sites corresponding to Infinium Type II... |
| meffil.get.x.sites | Get names of chromosome X CpG sites in the feature set. |
| meffil.get.y.sites | Get names of chromosome Y CpG sites in the feature set. |
| meffil.handle.outliers | Handle outliers in a methylation matrix |
| meffil.list.cell.type.references | List of available cell type references |
| meffil.list.chips | List of microarrays formats available. |
| meffil.list.cnv.references | List of available copy number references |
| meffil.list.featuresets | List of feature sets available. |
| meffil.load.controls | Load control probes |
| meffil.load.detection.pvalues | Load detection p-value matrix |
| meffil.load.raw.data | Load raw beta matrix |
| meffil.methylation.pcs | Compute principal components of a methylation matrix. |
| meffil.most.variable.cpgs | Most variable CpG sites |
| meffil.normalization.parameters | Specify parameters for testing normalization |
| meffil.normalization.parameters.from.betas | Specify parameters for testing normalization |
| meffil.normalization.report | Generate report on normalization performance |
| meffil.normalization.report.from.betas | Generate report on normalization performance |
| meffil.normalization.summary | Perform tests to check normalization performance |
| meffil.normalization.summary.from.betas | Perform tests to check normalization performance |
| meffil.normalize.dataset | Functional normalization |
| meffil.normalize.quantiles | Normalize microarray quantiles |
| meffil.normalize.sample | Normalize Infinium HumanMethylation450 BeadChip |
| meffil.normalize.samples | Normalize Infinium HumanMethylation450 BeadChips |
| meffil.pcs | Calculate control probe PCs |
| meffil.plot.beadnum.cpgs | Manhattan plot of number of beads by probe - percentage of... |
| meffil.plot.beadnum.samples | Plot number of beads per sample |
| meffil.plot.cell.counts | Cell count estimate quality plot |
| meffil.plot.control.batch | Test for association of control matrix probes with known... |
| meffil.plot.controlmeans | Plot the means of control probes for each sample and for each... |
| meffil.plot.control.scree | Plot scree plot of control matrix |
| meffil.plot.detectionp.cpgs | Manhattan plot of detection pval per probe - percentage with... |
| meffil.plot.detectionp.samples | Plot detection p values from idat files |
| meffil.plot.genotypes | Plot SNP beta and sample genotype concordances |
| meffil.plot.meth.unmeth | Plot average methylated vs unmethylated levels for each... |
| meffil.plot.pc.fit | Number of control matrix principal components |
| meffil.plot.probe.batch | Test normalized betas for association with known batch... |
| meffil.plot.probe.batch.from.betas | Test normalized betas for association with known batch... |
| meffil.plot.sex | Plot predicted sex |
| meffil.probe.info | Obtain a list of probes for a given feature set (chip). |
| meffil.qc | Perform QC on HumanMethylation450 idat files |
| meffil.qc.parameters | Specify parameters for QC |
| meffil.qc.report | Generate QC report |
| meffil.qc.summary | Perform QC analysis on idat files |
| meffil.read.samplesheet | Function to read Illumina "Sample Sheet" adapted from... |
| meffil.remove.samples | Remove samples from QC objects |
| meffil.save.detection.pvalues | Save detection p-value matrix to GDS file |
| meffil.snp.betas | Matrix of SNP 'beta' values |
| meffil.snp.concordance | Concordance between genotypes and SNP betas |
| meffil.snp.names | Obtain the list of identifiers for the SNPs on the... |
| meffil.summarize.relationship | Describe the relationship between two variables. |
