getAnnot {dmrseq} | R Documentation

## Retrieve annotation information

### Description

Uses the `annotatr` package to retrieve annotation information ( CpG category and gene coding sequences) for the `annoTrack` argument of `plotDMRs`. Allows for 5 re-tries if download fails (to allow for a spotty internet connection).

### Usage

    getAnnot(genomeName)

### Arguments

`genomeName` | a character object that indicates which organism is under study. Use the function `builtin_genomes()` to see a character vector of available genome names to choose from (see `annotatr` documentation for more details).

### Details

Note that this package needs to attach the `annotatr` package, and will return NULL if this cannot be done. You can still use the `plotDMRs` function without this optional annotation step, just by leaving the `annoTrack` argument as NULL.

### Value

a `SimpleGenomicRangesList` object with two elements returned by `getAnnot`. The first contains CpG category information in the first element (optional) coding gene sequence information in the second element (optional). At least one of these elements needs to be non-null in order for any annotation to be plotted, but it is not necessary to contain both.

### Examples

    # get annotation information for hg19
    annoTrack <- getAnnot('hg19')

[Package dmrseq version 1.2.5 Index]