Man pages for al2na/methylKit
DNA methylation analysis from high-throughput bisulfite sequencing results

adjustMethylCAdjust measured 5mC levels using 5hmC levels
assocComp-methodsAssociate principal components with sample annotations
bedgraph-methodsGet bedgraph from methylRaw, methylRawList and methylDiff...
calculateDiffMethDSS-methodscalculate Differential Methylation with DSS
calculateDiffMeth-methodsCalculate differential methylation statistics
clusterSamples-methodsHierarchical Clustering using methylation data The function...
dataSim-methodsSimulate DNA methylation data
diffMethPerChr-methodsGet and plot the number of hyper/hypo methylated...
extract-methodsextract parts of...
filterByCoverage-methodsFilter methylRaw, methylRawDB, methylRawList and...
genomation-deprecatedDeprecated/Defunct functions
getAssembly-methodsget assembly of the genome
getContext-methodsget the context of methylation
getCorrelation-methodsget correlation between samples in methylBase or methylBaseDB...
getCoverageStats-methodsget coverage stats from methylRaw object
getData-methodsget the data slot from the methylKit objects
getDBPath-methodsGet path to database of the methylDB objects
getMethylationStats-methodsget Methylation stats from methylRaw or methylRawDB object
getMethylDiff-methodsget differentially methylated regions/bases based on cutoffs
getSampleID-methodsGet or Set Sample-IDs of the methylKit objects
getTreatment-methodsGet or Set treatment vector of methylKit object
joinSegmentNeighboursJoin directly neighbouring segments produced by methSeg
makeMethylDB-methodscoerce methylKit objects from memory to flat file database...
methRead-methodsread file(s) to methylRaw or methylRawList objects
methSegSegment methylation or differential methylation profile
methSeg2bedExport segments to BED files
methylBase-classAn S4 class for methylation events sampled in multiple...
methylBaseDB-classAn S4 class for storing methylation events sampled in...
methylBase.objExample methylBase object.
methylDiff-classAn S4 class that holds differential methylation information
methylDiffDB-classAn S4 class that holds differential methylation information...
methylDiff.objExample methylKit objects.
methylRaw-classAn S4 class for holding raw methylation data from an...
methylRawDB-classAn S4 class for storing raw methylation data as flat file...
methylRawList-classAn S4 class for holding a list of methylRaw objects.
methylRawListDB-classAn S4 class for holding a list of methylRawDB objects.
methylRawList.objExample methylRawList object.
normalizeCoverage-methodsnormalize read coverage between samples
PCASamples-methodsPrincipal Components Analysis of Methylation data
percMethylation-methodsget percent methylation scores from methylBase or...
pool-methodsPool replicates within groups to a single sample per group
processBismarkAln-methodsGet methylation percentage from sorted Bismark alignments
reconstruct-methodsReconstruct methylBase or methylBaseDB object based on a new...
regionCountsGet regional counts for given GRanges or GRangesList object
removeComp-methodsRemove principal components from a methylBase object
reorganize-methodsReorganize methylKit objects by creating new objects from...
selectByOverlap-methodsselects records of methylDB objects lying inside a GRanges...
select-methodsselects rows from of methylKit objects
show-methodsshow method for methylKit classes
tileMethylCounts-methodsGet methylated/unmethylated base counts for tilling windows
unite-methodsunite methylRawList to a single table
updateMethObjectupdate methylKit objects The method updates object from...
al2na/methylKit documentation built on July 13, 2018, 12:07 a.m.