getAnnot: Retrieve annotation information

In kdkorthauer/dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

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 SimpleGRangesList 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')

kdkorthauer/dmrseq documentation built on April 2, 2022, 6:42 a.m.