summarize_categorical: Summarize categorical data over groupings of annotated...

In annotatr: Annotation of Genomic Regions to Genomic Annotations

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)

annotatr documentation built on Nov. 8, 2020, 8:16 p.m.