Description Usage Arguments Details Value Examples
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.
summarize_annotations(annotated_regions, annotated_random, quiet = FALSE)
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.
tbl_df of the number of regions per annotation type.
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### 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)
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