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

In rcavalcante/annotatr: Annotation of Genomic Regions to Genomic Annotations

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)

rcavalcante/annotatr documentation built on Aug. 22, 2024, 7:33 a.m.