methylPipe-package: Analysis of base-pair resolution DNA methylation data.
In methylPipe: Base resolution DNA methylation data analysis

Analysis of base-pair resolution DNA methylation data.

The package offers the following functionalities:

BSdata-class : This class is used in to point to a TABIX compressed file containing base-resolution DNA-methylation data and reference genome sequence
mCsmoothing : Smoothing and plotting methylation data, even chromosome wide
findPMDs : Find partially methylated regions for a given sample
mapBSdata2GRanges : Retrieve mC calls for a GRanges from a BSdata object for a sample
BSdataSet-class : This class is a set of BSdata objects
findDMR : Identifying differentially methylated regions for pairwise or multiple samples comparision
methstats : Descriptive methylation statistics of samples within BSdataSet object
consolidateDMRs : Joins differentially methylated regions according to their proximity to each other, statistical significance, methylation difference and DMR type
GEcollection-class : This class is used to define and manipulate a set of genomic regions and the associated DNA methylation patterns
getCpos : Get genomic Cxx positons for a series of genomic regions
getCposDensity : Determines the density of genomic Cxx positions for a series of genomic regions
profileDNAmetBin : Profile DNA methylation data for a set of genomic regions
plotMeth : Plot the methylation/omics data of a GEcollection object
BSprepare : Preparing tabular data to be used to feed a BSdata object
meth.call : Reads the methylation information from the sorted SAM files generated from BISMARK aligner
pool.reads : Combine reads of replicates within a group
GElist-class : This class is a set of GEcollection objects