RnBDiffMeth-class {RnBeads} | R Documentation

## RnBDiffMeth Class

### 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

[Package RnBeads version 1.12.1 Index]