Compute the nearest annotation to the annoated genes in brainflowprobes

For a given set of genomic regions, this function computes the nearest annotation information using the Annotated Genes required by this package. The Annotated Genes are actually provided by GenomicState::GenomicStateHub().

get_nearest_annotation(gr, CODING_ONLY = FALSE)

Arguments

gr

A GenomicRanges::GRanges() object.

CODING_ONLY

A logical vector of length 1 specifying whether to subset the Annotated Genes to only the coding genes. That is, whether to subset the genes by whether they have a non-NA CSS value. The Annotated Genes are downloaded with GenomicState::GenomicStateHub().

Value

The bumphunter::matchGenes() output for the annotation information using the Annotated Genes for Gencode version 31 on hg19 coordinates (subset to only the coding elements if CODING_ONLY was set to TRUE).

Details

This is an utility function used by region_info, four_panels and plot_coverage.

Author

Leonardo Collado-Torres

Examples

gr <- GenomicRanges::GRanges("chr10:135379301-135379311:+")

get_nearest_annotation(gr)
#> loading from cache
#>   name annotation description region distance   subregion insideDistance
#> 1 <NA>       <NA> inside exon inside        0 inside exon              0
#>   exonnumber nexons                         UTR strand geneL codingL
#> 1          1      5 inside transcription region      + 63710      NA
#>            Geneid subjectHits
#> 1 ENSG00000288107       62226
get_nearest_annotation(gr, CODING_ONLY = TRUE)
#> loading from cache
#>     name          annotation description     region distance subregion
#> 1 CYP2E1 NM_000773 NP_000764  downstream downstream    45391      <NA>
#>   insideDistance exonnumber nexons  UTR strand geneL codingL          Geneid
#> 1             NA         NA     12 <NA>      + 40814   11568 ENSG00000130649
#>   subjectHits
#> 1        6233