summarize_annotations: Summarize annotation counts

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

Summarize annotation counts

Description

Given a GRanges of annotated regions, count the number of regions in each annotation type. If annotated_random is not NULL, then the same is computed for the random regions.

Usage

summarize_annotations(annotated_regions, annotated_random, quiet = FALSE)

Arguments

annotated_regions	The GRanges result of annotate_regions().
annotated_random	The GRanges result of annotate_regions() on the randomized regions created from randomize_regions().
quiet	Print progress messages (FALSE) or not (TRUE).

Details

If a region is annotated to multiple annotations of the same annot.type, the region will only be counted once. For example, if a region were annotated to multiple exons, it would only count once toward the exons, but if it were annotated to an exon and an intron, it would count towards both.

Value

A tbl_df of the number of regions per annotation type.

Examples

   ### An example of ChIP-seq peaks with signalValue

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

   file = system.file('extdata', 'Gm12878_Stat3_chr2.bed.gz', package = 'annotatr')
   r = read_regions(con = file, genome = 'hg19')

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

   rnd = randomize_regions(regions = r)

   rnd_annots = annotate_regions(
       regions = rnd,
       annotations = annotations,
       ignore.strand = TRUE,
       quiet = FALSE)

   # Summarize the annotated regions without randomized regions
   s = summarize_annotations(annotated_regions = a)

   # Summarize the annotated regions with randomized regions
   s_rnd = summarize_annotations(
       annotated_regions = a,
       annotated_random = rnd_annots)

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