A class for storing differential methylation data.
Contains differential methylation tables (DMT) for multiple comparisons and region types. DMTs can be stored in memory as R objects or on disk
List of differential methylation tables on site level (see
computeDiffMeth.bin.site for details).
Indexed by comparison.
List of lists of differential methylation tables on region levels (see
computeDiffMeth.bin.region for details).
Indexed by region type on the top level and comparison on the lower level.
character vector of all comparisons stored in the objects. Vector indices correspond to indices in the
regions list slots.
character vector of all region types stored in the objects. Vector indices correspond to indices in
regions list slot.
A character matrix with 2 columns containing group labels of all comparisons in the object
A list containing comparison information for each comparison. See
get.comparison.info for details.
Logical indicating whether the object contains site-level differential methylation information.
method which was applied to obtain the site-level p-values.
method to be used to detect differentially variable sites.
coverage threshold. Important for certain columns of the differential methylation tables.
Flag indicating whether the tables should be stored on disk rather than in the main memory
path on the disk for DMTs.Only meaningful if
remove tables stored to disk from the file system
Gets all region types represented in the object as character vector
Gets all comparisons represented in the object as character vector
Gets all comparison group names as a matrix
Gets the coverage threshold employed for obtaining statistics in the differential methylation tables
Gets a differential methylation table
Adds a differential methylation table
relink disk dumped tables. Useful if the files are manually copied or if the object is loaded again
save disk dumped tables as binaries and zip them. Useful if the files are copied or shared.
Merges two disjoint RnBDiffMeth objects into one
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