API for tectronics/methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results

Global functions
CpG.dinuc.unify Source code
PCASamples Man page
PCASamples,methylBase-method Man page
QValuesfun Source code
SLIMfunc Source code
[ Man page
[,methylBase-method Man page
[,methylDiff-method Man page
[,methylRaw-method Man page
adjlim Source code
adjust.methylC Man page
adjust.methylC,methylRaw,methylRaw-method Man page
adjust.methylC,methylRawList,methylRawList-method Man page
annotate.WithFeature Man page
annotate.WithFeature,GRanges,GRanges-method Man page
annotate.WithFeature,methylDiff,GRanges-method Man page
annotate.WithFeature.Flank Man page
annotate.WithFeature.Flank,GRanges,GRanges,GRanges-method Man page
annotate.WithFeature.Flank,methylDiff,GRanges,GRanges-method Man page
annotate.WithGenicParts Man page
annotate.WithGenicParts,GRanges,GRangesList-method Man page
annotate.WithGenicParts,methylDiff,GRangesList-method Man page
annotate.gr.WithGenicParts Source code
annotationByFeature Man page
annotationByFeature-class Man page
annotationByGenicParts Man page
annotationByGenicParts-class Man page
assocComp Man page Source code
bed12.to.exons Source code
bed12.to.introns Source code
bedgraph Man page
bedgraph,methylDiff-method Man page
bedgraph,methylRaw-method Man page
bedgraph,methylRawList-method Man page
calculateDiffMeth Man page
calculateDiffMeth,methylBase-method Man page
check.bed.validity Source code
check.pipeline.list Source code
cluster Source code
clusterSamples Man page
clusterSamples,methylBase-method Man page
colSds Source code
diffMethPerChr Man page
diffMethPerChr,methylDiff-method Man page
dist.cor Source code
distance2nearestFeature Source code
extract Man page
f1 Source code
fast.fisher Source code
filterByCoverage Man page
filterByCoverage,methylRaw-method Man page
filterByCoverage,methylRawList-method Man page
fix.q.values.fisher Source code
fix.q.values.glm Source code
get.methylDiff Man page
get.methylDiff,methylDiff-method Man page
getAssembly Man page
getAssembly,methylBase-method Man page
getAssembly,methylDiff-method Man page
getAssembly,methylRaw-method Man page
getAssociationWithTSS Man page
getAssociationWithTSS,annotationByGenicParts-method Man page
getContext Man page
getContext,methylBase-method Man page
getContext,methylDiff-method Man page
getContext,methylRaw-method Man page
getCorrelation Man page
getCorrelation,-methods Man page
getCorrelation,methylBase-method Man page
getCorrelation-method Man page
getCoverageStats Man page
getCoverageStats,methylRaw Man page
getCoverageStats,methylRaw-method Man page
getData Man page
getData,-methods Man page
getData,methylBase-method Man page
getData,methylDiff-method Man page
getData,methylRaw-method Man page
getData-method Man page
getFeatsWithTargetsStats Man page
getFeatsWithTargetsStats,annotationByFeature-method Man page
getFlanks Man page
getFlanks,GRanges-method Man page
getMembers Man page
getMembers,annotationByFeature-method Man page
getMethylationStats Man page
getMethylationStats,methylRaw-method Man page
getTargetAnnotationStats Man page
getTargetAnnotationStats,annotationByFeature-method Man page
glm.set Source code
glm.set.mc Source code
glm.set.mc.v1 Source code
glm.set.v1 Source code
mc.fish Source code
merge2 Source code
methylBase Man page
methylBase-class Man page
methylBase.obj Man page
methylDiff Man page
methylDiff-class Man page
methylDiff.obj Man page
methylRaw Man page
methylRaw-class Man page
methylRawList Man page
methylRawList-class Man page
methylRawList.obj Man page
nearest.2bed Source code
normalizeCoverage Man page
normalizeCoverage,methylRawList-method Man page
pcaPlot Source code
pcaPlotT Source code
percMethylation Man page
percMethylation,methylBase-method Man page
plotTargetAnnotation Man page
plotTargetAnnotation,annotationByFeature-method Man page
pool Man page
pool,methylBase-method Man page
read Man page
read,character,character,character-method Man page
read,list,list,character-method Man page
read.bed Man page
read.bed,character-method Man page
read.bismark Man page
read.bismark,character,character,character-method Man page
read.bismark,list,list,character-method Man page
read.feature.flank Man page
read.feature.flank,character-method Man page
read.transcript.features Man page
read.transcript.features,character-method Man page
readTableFast Source code
reconstruct Man page Source code
regionCounts Man page
regionCounts,methylBase,GRanges-method Man page
regionCounts,methylRaw,GRanges-method Man page
regionCounts,methylRaw,GRangesList-method Man page
regionCounts,methylRawList,GRanges-method Man page
regionCounts,methylRawList,GRangesList-method Man page
removeComp Man page Source code
reorganize Man page
reorganize,methylBase-method Man page
reorganize,methylRawList-method Man page
rowSds Source code
select Man page
select,methylBase-method Man page
select,methylDiff-method Man page
select,methylRaw-method Man page
show Man page
show,annotationByFeature-method Man page
show,annotationByGenicParts-method Man page
show,methylBase Man page
show,methylDiff Man page
show,methylRaw Man page
show,methylRawList Man page
structureAMPoutput Source code
structureGeneric Source code
tileMethylCounts Man page
tileMethylCounts,methylBase-method Man page
tileMethylCounts,methylRaw-method Man page
tileMethylCounts,methylRawList-method Man page
unite Man page
unite,-methods Man page
unite,methylRawList-method Man page
updateMethObject Man page
updateMethObject,methylBase-method Man page
updateMethObject,methylDiff-method Man page
updateMethObject,methylRaw-method Man page
updateMethObject,methylRawList-method Man page
valid.methylRawObj Source code
tectronics/methylkit documentation built on May 27, 2017, 4:14 a.m.