summarize_annotations {annotatr} | R Documentation

## 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)

[Package annotatr version 1.4.1 Index]