Principal Components Analysis of Methylation data
Adjust measured 5mC levels using 5hmC levels
Associate principal components with sample annotations
Get bedgraph from methylRaw, methylRawList and methylDiff objects
calculate Differential Methylation with DSS
Hierarchical Clustering using methylation data The function clusters samples using 'hclust' function and various distance metrics derived from percent methylation per base or per region for each sample.
Get and plot the number of hyper/hypo methylated regions/bases per chromosome
extract parts of methylRaw,methylRawDB,methylBase,methylBaseDB and methylDiff data
Filter methylRaw, methylRawDB, methylRawList and methylRawListDB object based on read coverage
get correlation between samples in methylBase or methylBaseDB object
get coverage stats from methylRaw object
Get path to database of the methylDB objects
get the data slot from the methylKit objects
get differentially methylated regions/bases based on cutoffs
get Methylation stats from methylRaw or methylRawDB object
Get or Set Sample-IDs of the methylKit objects
Get or Set treatment vector of methylKit object
Join directly neighbouring segments produced by methSeg
coerce methylKit objects from memory to flat file database objects
read file(s) to methylRaw or methylRawList objects
Segment methylation or differential methylation profile
An S4 class for methylation events sampled in multiple experiments
An S4 class for storing methylation events sampled in multiple experiments as flat file database
An S4 class that holds differential methylation information
An S4 class that holds differential methylation information as flat file database
An S4 class for holding raw methylation data from an alignment pipeline.
An S4 class for storing raw methylation data as flat file database.
An S4 class for holding a list of methylRaw objects.
An S4 class for holding a list of methylRawDB objects.
get percent methylation scores from methylBase or methylBaseDB object
Pool replicates within groups to a single sample per group
Get methylation percentage from sorted Bismark alignments
Reconstruct methylBase or methylBaseDB object based on a new methylation percentage matrix
Get regional counts for given GRanges or GRangesList object
Remove principal components from a methylBase object
Reorganize methylKit objects by creating new objects from subset of samples
selects records of methylDB objects lying inside a GRanges range
Get methylated/unmethylated base counts for tilling windows
update methylKit objects The method updates object from earlier versions (<v0.9.1) to latest object.