get_nearest_annotation: Compute the nearest annotation to the annoated genes in...

In brainflowprobes: Plots and annotation for choosing BrainFlow target probe sequence

Description

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().

Usage

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().

Details

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

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).

Author(s)

Leonardo Collado-Torres

Examples

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

get_nearest_annotation(gr)
get_nearest_annotation(gr, CODING_ONLY = TRUE)

brainflowprobes documentation built on Dec. 21, 2020, 2:01 a.m.