Files in perishky/meffil
Efficient algorithms for DNA methylation

DESCRIPTION
LICENSE
NAMESPACE
R/adjust.r R/background-correct.r R/basenames.r R/cell-count-qc-plots.r R/cell-counts.r R/cell-type-references.r R/cell-type-specific-methylation.r R/check-data-frame.r R/cnv-matrix.r R/cnv-references.r R/cnv.r R/create-qc-object.r R/create-samplesheet.r R/design-matrix.r R/dye-bias-correct.r R/estimate-cell-counts.r R/ewas-report.r R/ewas-variable-summaries.r R/ewas.r R/extract-beadnum.r R/extract-controls.r R/extract-detection-pvalues.r R/extract-from-samplesheet.r R/extract-genotypes.r R/features.r R/get-beta.r R/globals.r R/impute-matrix.r R/isva.r R/knit-report.r R/load-controls.r R/load-detection-pvalues.r R/load-raw-betas.r R/manifest.r R/mclapply.r R/methylation-pcs.r R/most-variable.r R/msg.r R/normalization-report.r R/normalize-dataset.r R/normalize-quantiles.r R/normalize-sample.r R/normalize-samples.r R/plot-ewas.r R/plot-pc-fit.r R/qc-report.r R/qc.r R/read-samplesheet.r R/rg-to-mu.r R/rg.r R/simplify-variable.r R/site-subsets.r R/snp-betas.r R/snp-concordance.r R/winsorize.r data-raw/andrews-bakulski-reference.r
data-raw/chen-table-e2.csv
data-raw/epic-excludes.txt
data-raw/geo.r data-raw/gervin-lyle-reference.r data-raw/globals.r data-raw/gse35069-references.r data-raw/gse68456-reference.r data-raw/load-450k-manifest.r data-raw/load-epic-manifest.r data-raw/saliva-reference.r docs/meffil.pdf
docs/meta-analysis.png
docs/workflow.png
inst/cnv.rda
inst/featuresets.rda
inst/probes.rda
inst/references.rda
inst/reports/blank.rmd inst/reports/cell-counts.rmd inst/reports/cpg-plot.rmd inst/reports/ewas-covariate.rmd inst/reports/ewas-report.rmd inst/reports/genotype-concordance.rmd inst/reports/manhattan-plot.rmd inst/reports/missing.rmd inst/reports/normalization-report.rmd inst/reports/plot.rmd inst/reports/qc-report.rmd inst/reports/qq-plot.rmd inst/reports/wide-plot.rmd install-automatic.r install-manual.r man/guess.batch.vars.Rd man/meffil.add.cell.type.reference.Rd man/meffil.add.chip.Rd man/meffil.add.cnv.reference.Rd man/meffil.add.copynumber450k.references.Rd man/meffil.add.featureset.Rd man/meffil.basenames.Rd man/meffil.calculate.cnv.Rd man/meffil.cell.count.estimates.Rd man/meffil.cell.count.qc.plots.Rd man/meffil.cell.type.specific.methylation.Rd man/meffil.cnv.matrix.Rd man/meffil.control.matrix.Rd man/meffil.create.qc.object.Rd man/meffil.create.samplesheet.Rd man/meffil.design.matrix.Rd man/meffil.estimate.cell.counts.Rd man/meffil.estimate.cell.counts.from.betas.Rd man/meffil.ewas.Rd man/meffil.ewas.covariate.associations.Rd man/meffil.ewas.cpg.plot.Rd man/meffil.ewas.manhattan.plot.Rd man/meffil.ewas.parameters.Rd man/meffil.ewas.qq.plot.Rd man/meffil.ewas.report.Rd man/meffil.ewas.sample.characteristics.Rd man/meffil.ewas.summary.Rd man/meffil.extract.genotypes.Rd man/meffil.featureset.Rd man/meffil.get.autosomal.sites.Rd man/meffil.get.beta.Rd man/meffil.get.features.Rd man/meffil.get.sites.Rd man/meffil.get.typeii.sites.Rd man/meffil.get.x.sites.Rd man/meffil.get.y.sites.Rd man/meffil.list.cell.type.references.Rd man/meffil.list.chips.Rd man/meffil.list.cnv.references.Rd man/meffil.list.featuresets.Rd man/meffil.load.controls.Rd man/meffil.load.detection.pvalues.Rd man/meffil.load.raw.data.Rd man/meffil.methylation.pcs.Rd man/meffil.most.variable.cpgs.Rd man/meffil.normalization.parameters.Rd man/meffil.normalization.report.Rd man/meffil.normalization.summary.Rd man/meffil.normalize.dataset.Rd man/meffil.normalize.quantiles.Rd man/meffil.normalize.sample.Rd man/meffil.normalize.samples.Rd man/meffil.pcs.Rd man/meffil.plot.beadnum.cpgs.Rd man/meffil.plot.beadnum.samples.Rd man/meffil.plot.cell.counts.Rd man/meffil.plot.control.batch.Rd man/meffil.plot.control.scree.Rd man/meffil.plot.controlmeans.Rd man/meffil.plot.detectionp.cpgs.Rd man/meffil.plot.detectionp.samples.Rd man/meffil.plot.genotypes.Rd man/meffil.plot.meth.unmeth.Rd man/meffil.plot.pc.fit.Rd man/meffil.plot.probe.batch.Rd man/meffil.plot.sex.Rd man/meffil.probe.info.Rd man/meffil.qc.Rd man/meffil.qc.parameters.Rd man/meffil.qc.report.Rd man/meffil.qc.summary.Rd man/meffil.read.samplesheet.Rd man/meffil.remove.samples.Rd man/meffil.snp.betas.Rd man/meffil.snp.concordance.Rd man/meffil.snp.names.Rd man/meffil.summarize.relationship.Rd readme.md regenerate.r tests/450k-and-epic.rmd tests/450k-demo.rmd
tests/AdditionalFile3.csv
tests/GSE86831.rmd
tests/Makefile
tests/cnv.rmd tests/cord.rmd tests/dataset-450k-demo.r tests/dataset-450k-demo.rmd tests/dataset-450k-lead.r tests/dataset-450k-lead.rmd tests/dataset-epic-demo.r tests/dataset-epic-demo.rmd tests/epic-demo.rmd tests/ewas.rmd
tests/fix-minfi-control-matrix.patch
tests/gds.rmd
tests/hannum.txt
tests/html/450k-and-epic.html
tests/html/450k-demo.html
tests/html/GSE86831.html
tests/html/cord.html
tests/html/epic-demo.html
tests/html/ewas.html
tests/html/gds.html
tests/html/minfi.html
tests/html/random.html
tests/knit.r tests/minfi.rmd tests/random.rmd
todo.txt
perishky/meffil documentation built on Dec. 3, 2019, 2:05 a.m.