GRanges of annotated regions, count the number of regions when the annotations are grouped
by categorical columns.
A character vector to group the data in
Print progress messages (FALSE) or not (TRUE).
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.
dplyr::tbl_df of the counts of groupings according to the
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# 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)
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