RnBDiffMeth-class: RnBDiffMeth Class

Description Details Slots Methods Author(s)

Description

A class for storing differential methylation data.

Details

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

Slots

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.

variability.method

method to be used to detect differentially variable sites.

covg.thres

coverage threshold. Important for certain columns of the differential methylation tables.

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

Methods

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

Author(s)

Fabian Mueller


RnBeads documentation built on March 3, 2021, 2 a.m.