merge_classes {DMRforPairs} | R Documentation

## MERGE ILLUMINA PROBE CLASSES

### Description

Illumina assigns quite specific functional classes to the probes. 11 classes are defined (Bibikova et al. 2009 & 2011):

- Relation to gene: Body, 5'UTR, 3'UTR, 1stExon, TSS1500, TSS200

- Relation to CpG island: Island, N_Shelf, N_Shore, S_Shelf, S_Shore

As DMRforPairs looks at probes in close proximity to each other within each class, very specific annotations might result in too few probes per region per class and a subsequent drop in the number of identified regions and/or statistical power. This function therefore allows grouping and / or selection of classes of interest.

### Usage

    merge_classes(refgene_class,island_class,recode=1,sep=";")

### Arguments

`refgene_class` | see description and classes_gene parameter in `DMRforPairs`
`island_class` | see description and classes_island parameter in `DMRforPairs`
`recode` | recoding scheme to use for the functional classes. Can be custom scheme (data frame) or build in scheme (0, 1 or 2). See details.
`sep` | Separator used in the second column of the recode parameter. Use ";" or do not specify if using the build in schemes.

### Details

The recode parameter can be set to use one of the build in recoding schemes:

- 0: analyze all 11 classes annotated by Illumina separately

- 1: group Body, 5'UTR, 3'UTR into one category "gene" and TSS1500 and TSS200 in another ("tss"). All island associated classes are merged in one class "island"

- 2: all probes without subdivision into classes (also included probes associated with no class).

The recode parameter can also be set to a custom recoding scheme (data.frame). For example:
data.frame(c("gene","tss"),c("Body;5\'UTR;3\'UTR;1stExon","TSS1500;TSS200")).
In this scheme the classes are merged into two categories: TSS or other gene region. Probes solely associated with CpG island-related classes are discarded. Probes not annotated to any of the 11 classes are always discarded by DMRforPairs, except when option 2 is used which collects all probes into one class (i.e. ignores classes).
If classes are unknown an m x 1 character vector with "unknown.gene" and "unknown.island" for all m rows (probes) can be used for the refgene_class and island_class parameters respectively (set "recode" to 2!).

### Value

List of objects containing:

`$pclass` | original classes per probe (gene and island classes are merged) (m x 1 data frame)
`$pclass_merged` | classes after recoding (m x 1 data frame)
`$no.pclass` | row indexes of probes with no annotation to any of the classes specified in the recoding scheme.
`$u_pclass` | unique list of the classes of interest after recoding (i.e. the first column of the recode data fram)

### Author(s)

Martin Rijlaarsdam, m.a.rijlaarsdam@gmail.com

### References

- Bibikova, M., et al., High density DNA methylation array with single CpG site resolution. Genomics, 2011. 98(4): p. 288-95.

- Bibikova, M., et al., Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics, 2009. 1(1): p. 177-200.

### Examples

    #merge_classes() is an integrated part of the DMRforPairs() wrapper and is
    #not usually called by the user directly. Please see DMRforPairs() for
    #an example.

[Package DMRforPairs version 1.20.0 Index]