Function reference • valr

Data types
`tbl_genome()` `trbl_genome()`	Tibble for reference sizes.
`tbl_interval()` `trbl_interval()`	Tibble for intervals.
`is.tbl_genome()`	Test if the object is a tbl_genome.
`is.tbl_interval()`	Test if the object is a tbl_interval.
`as.tbl_genome()`	Coerce objects to tbl_genome.
`as.tbl_interval()`	Coerce objects to tbl_intervals.
Load data
`read_bed()` `read_bed12()` `read_bedgraph()` `read_narrowpeak()` `read_broadpeak()`	Read BED and related files.
`read_genome()`	Read genome files.
`read_vcf()`	Read a VCF file.
`db_ucsc()` `db_ensembl()`	Fetch data from remote databases.
Single set operations
`bed_cluster()`	Cluster neighboring intervals.
`bed_complement()`	Identify intervals in a genome not covered by a query.
`bed_flank()`	Create flanking intervals from input intervals.
`bed_merge()`	Merge overlapping intervals.
`bed_partition()`	Partition intervals into elemental intervals
`bed_slop()`	Increase the size of input intervals.
`bed_shift()`	Adjust intervals by a fixed size.
`bed_sort()`	Sort a set of intervals.
Multiple set operations
`bed_closest()`	Identify closest intervals.
`bed_coverage()`	Compute coverage of intervals.
`bed_intersect()`	Identify intersecting intervals.
`bed_map()` `concat()` `values_unique()` `values()`	Calculate summaries from overlapping intervals.
`bed_subtract()`	Subtract two sets of intervals.
`bed_window()`	Identify intervals within a specified distance.
Randomizing intervals
`bed_random()`	Generate randomly placed intervals on a genome.
`bed_shuffle()`	Shuffle input intervals.
Interval statistics
`bed_absdist()`	Compute absolute distances between intervals.
`bed_reldist()`	Compute relative distances between intervals.
`bed_fisher()`	Fisher's test to measure overlap between two sets of intervals.
`bed_jaccard()`	Calculate the Jaccard statistic for two sets of intervals.
`bed_projection()`	Projection test for query interval overlap.
Utilities
`create_introns()`	Create intron features.
`create_tss()`	Create transcription start site features.
`create_utrs3()`	Create 3' UTR features.
`create_utrs5()`	Create 5' UTR features.
`bed_makewindows()`	Divide intervals into new sub-intervals ("windows").
`bed12_to_exons()`	Convert BED12 to individual exons in BED6.
`bed_glyph()`	Create example glyphs for valr functions.
`bound_intervals()`	Select intervals bounded by a genome.
`flip_strands()`	Flip strands in intervals.
`interval_spacing()`	Calculate interval spacing.
`valr_example()`	Provide working directory for valr example files.

Reference

Data types

Load data

Single set operations

Multiple set operations

Randomizing intervals

Interval statistics

Utilities

Contents