R: A function to intersect user region data with annotation data

annotate_regions {annotatr}

R Documentation

A function to intersect user region data with annotation data

Description

Annotate genomic regions to selected genomic annotations while preserving the data associated with the genomic regions.

Usage

annotate_regions(regions, annotations, minoverlap = 1L,
  ignore.strand = TRUE, quiet = FALSE)

Arguments

`regions`	The GRanges object returned by `read_regions()`.
`annotations`	A character vector of annotations to build. Valid annotation codes are listed with `builtin_annotations()`. The "basicgenes" shortcut builds the following regions: 1-5Kb upstream of TSSs, promoters, 5UTRs, exons, introns, and 3UTRs. The "cpgs" shortcut builds the following regions: CpG islands, shores, shelves, and interCGI regions. NOTE: Shortcuts need to be appended by the genome, e.g. `hg19_basicgenes`. Custom annotations whose names are of the form `[genome]_custom_[name]` should also be included. Custom annotations should be read in and converted to `GRanges` with `read_annotations()`. They can be for a `supported_genome()`, or for an unsupported genome.
`minoverlap`	A scalar, positive integer, indicating the minimum required overlap of regions with annotations.
`ignore.strand`	Logical indicating whether strandedness should be respected in findOverlaps(). Default FALSE.
`quiet`	Print progress messages (FALSE) or not (TRUE).

Value

A GRanges where the granges are from the regions, and the mcols include the mcols from the regions and a column with the annotation GRanges.

Examples

   r_file = system.file('extdata', 'test_read_multiple_data_nohead.bed', package='annotatr')
   extraCols = c(pval = 'numeric', mu1 = 'integer', mu0 = 'integer', diff_exp = 'character')
   r = read_regions(con = r_file, extraCols = extraCols, rename_score = 'coverage')

   # Get premade CpG annotations
   data('annotations', package = 'annotatr')

   a = annotate_regions(
       regions = r,
       annotations = annotations,
       ignore.strand = TRUE)

[Package annotatr version 1.4.1 Index]