RnBDiffMeth-class: RnBDiffMeth Class

Description

A class for storing differential methylation data.

sites: List of differential methylation tables on site level (see computeDiffMeth.bin.site for details). Indexed by comparison.
regions: 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.
comparisons: character vector of all comparisons stored in the objects. Vector indices correspond to indices in the sites and regions list slots.
region.types: character vector of all region types stored in the objects. Vector indices correspond to indices in the regions list slot.
comparison.grouplabels: A character matrix with 2 columns containing group labels of all comparisons in the object
comparison.info: A list containing comparison information for each comparison. See get.comparison.info for details.
includesSites: Logical indicating whether the object contains site-level differential methylation information.
site.test.method: method which was applied to obtain the site-level p-values.
covg.thres: coverage threshold. Important for certain columns of the differential methylation tables. See computeDiffMeth.bin.site and computeDiffMeth.bin.region for details.
disk.dump: Flag indicating whether the tables should be stored on disk rather than in the main memory
disk.path: path on the disk for DMTs.Only meaningful if disk.dump is TRUE

destroy,RnBDiffMeth-method: remove tables stored to disk from the file system
get.region.types,RnBDiffMeth-method: Gets all region types represented in the object as character vector
get.comparisons,RnBDiffMeth-method: Gets all comparisons represented in the object as character vector
get.comparison.grouplabels,RnBDiffMeth-method: Gets all comparison group names as a matrix
get.covg.thres,RnBDiffMeth-method: Gets the coverage threshold employed for obtaining statistics in the differential methylation tables
get.table,RnBDiffMeth-method: Gets a differential methylation table
addDiffMethTable,RnBDiffMeth-method: Adds a differential methylation table
reload,RnBDiffMeth-method: relink disk dumped tables. Useful if the files are manually copied or if the object is loaded again
save.tables,RnBDiffMeth-method: save disk dumped tables as binaries and zip them. Useful if the files are copied or shared.
join.diffMeth: Merges two disjoint RnBDiffMeth objects into one

Contains differential methylation tables (DMT) for multiple comparisons and region types. DMTs can be stored in memory as R objects or on disk