API for perishky/meffil
Efficient algorithms for DNA methylation

Global functions
.onLoad Source code
EstDimRMT 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
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 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.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
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
lmfit.safer 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.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.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.covariate.associations Man page Source code
meffil.ewas.cpg.plot Man page Source code
meffil.ewas.manhattan.plot 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.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.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.report Man page Source code
meffil.normalization.summary 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.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.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
qq.lambda Source code
quantile.normalize.betas Source code
quantile.normalize.signals Source code
read.idat Source code
read.rg 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
perishky/meffil documentation built on Dec. 3, 2019, 2:05 a.m.