summarize_categorical {annotatr} | R Documentation

## Summarize categorical data over groupings of annotated regions

### Description

Given a `GRanges` of annotated regions, count the number of regions when the annotations are grouped `by` categorical columns.

### Usage

    summarize_categorical(annotated_regions, by = c("annot.type", "annot.id"),
      quiet = FALSE)

### Arguments

`annotated_regions` | The `GRanges` result of `annotate_regions()`.
`by` | A character vector to group the data in `as.data.frame(annotated_regions)` by and tally over. Default is `c('annot.type', 'annot.id')`.
`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 grouped `dplyr::tbl_df` of the counts of groupings according to the `by` vector.

### Examples

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

       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, genome = 'hg19', extraCols = extraCols, rename_score = 'coverage')

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

       sc = summarize_categorical(
           annotated_regions = a,
           by = c('annot.type', 'name'),
           quiet = FALSE)

[Package annotatr version 1.13.1 Index]