Package index • bedscout

All functions

annotate_nearby_features(): Annotates a GRanges object with nearby features in another GRanges object
annotate_nearest_features(): Annotate the closest feature
annotate_overlapping_features(): Annotates a GRanges object with overlapping features in another GRanges object
calculate_venn_intersections(): Calculates all intersections in a list of GRanges object for a venn diagram of an arbitrary number of elements.
combinations_enrichment(): Calculate enrichment combinations of different elements within a list
combinations_score(): Apply a given score function to all pairs in a list of GRanges objects
.intersect_subset(): Intersection of a list of GRanges filtering by index. The use of this is to be able to map by powerset
.key_value_string(): Make a string out of a named list.
.limited_size_caption_line(): Make a string out of a named list. Split into lines if too wide.
.make_venn_names(): Make names for intersections according to index list
.package_caption(): Make a string to put as caption in verbose mode. Includes system date.
.powerset(): Calculates all possible subsets of a list of elements
fc_enrichment(): Calculate fold change enrichment of a GRanges object's overlap with another GRanges object based on genome size.
fit_euler(): Find a fit for a set of intersections in the form of an euler object.
gr_universe(): GRanges universe for a set of conditions and replicates
grlist_intersect(): Find the intersection of a list of GRanges objects.
grlist_intersect_size(): Calculate the size of the intersection of a list of GRanges objects.
import_named_bed_into_list(): Make a named bed into a list of GRanges objects to be used with pairwise functions, mostly.
impute_feature(): Annotate each locus in a GRanges with the best overlap in another feature GRanges. Best overlap is calculated as jaccard index:
jaccard_index(): Calculate jaccard index between two GenomicRanges objects.
loci_consensus(): Find a consensus set of loci across a set of GRanges objects.
loci_overlap(): Calculate the number of loci that overlap between two GRanges objects (ignoring length).
pairwise_enrichment(): Calculate pairwise enrichment matrix between two lists of GRanges objects
pairwise_score(): Apply a given score function to all pairwise combinations of two named GRanges lists
peaks_universe(): Peaks universe for a set of conditions and replicates
plot_combinations_score(): Plot triangular pairwise enrichment heatmap for a single GRanges list
plot_euler(): Plot a Euler diagram with intersections between GRanges objects
plot_pairwise_score(): Plot pairwise enrichment heatmap
total_bp_overlap(): Total overlapping base pairs between two GRanges objects.