Man pages for fortunatobianconi/methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results

adjust.methylCAdjust measured 5mC levels using 5hmC levels
annotate.WithFeature.Flank-methodsAnnotate an object with two sets of genomic features
annotate.WithFeature-methodsAnnotate object with a set of genomic features
annotate.WithGenicParts-methodsAnnotate given object with gene annotation
annotationByFeature-classAn S4 class for overlap of target features with a generic...
annotationByGenicParts-classAn S4 class for overlap of target features with gene...
annotationByGenicParts-methodsGet distance to nearest TSS and gene id from...
assocComp-methodsAssociate principal components with sample annotations
bedgraph-methodsGet bedgraph from methylRaw, methylRawList and methylDiff...
calculateDiffMeth-methodsCalculate differential methylation statistics
clusterSamples-methodsHierarchical Clustering using methylation data
diffMethPerChr-methodsGet and plot the number of hyper/hypo methylated...
extract-methodsextract parts of methylRaw,methylBase and methylDiff data
filterByCoverage-methodsFilter methylRaw and methylRawList object based on read...
getAssembly-methodsget assembly of the genome
getContext-methodsget the context of methylation
getCorrelation-methodsget correlation between samples in methylBase object
getCoverageStats-methodsget coverage stats from methylRaw object
getData-methodsget the data slot from the methylKit objects
getFeatsWithTargetsStats-methodsGet the percentage/count of annotation features overlapping...
getFlanks-methodsGet upstream and downstream adjacent regions to a genomic...
getMembers-methodsGet the membership slot of annotationByFeature
getMethylationStats-methodsget Methylation stats from methylRaw object
get.methylDiff-methodsget differentially methylated regions/bases based on cutoffs
getTargetAnnotationStats-methodsGet the percentage of target features overlapping with...
methylBase-classAn S4 class for methylation events sampled in multiple...
methylBase.objExample methylBase object.
methylDiff-classAn S4 class that holds differential methylation information
methylDiff.objExample methylKit objects.
methylRaw-classAn S4 class for holding raw methylation data from an...
methylRawList-classAn S4 class for holding a list of methylRaw 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 object
plotTargetAnnotation-methodsPlot annotation categories from annotationByGenicParts or...
pool-methodsPool replicates within groups to a single sample per group
read.bed-methodsread a bed file and convert it to GRanges
read.bismark-methodsRead from sorted Bismark SAM files
read.feature.flank-methodsa function to read-in genomic features and their upstream and...
read-methodsread file(s) to a methylrawList or methylraw object
read.transcript.features-methodsRead transcript features from a BED file
reconstruct-methodsReconstruct methylBase object based on a new methylation...
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...
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
fortunatobianconi/methylkit documentation built on May 16, 2019, 1:51 p.m.