Data types 


Tibble for reference sizes. 

Tibble for intervals. 

Test if the object is a tbl_genome. 

Test if the object is a tbl_interval. 

Coerce objects to tbl_genome. 

Coerce objects to tbl_intervals. 

Load data 


Read BED and related files. 
Read genome files. 

Read a VCF file. 

Fetch data from remote databases. 

Single set operations 

Cluster neighboring intervals. 

Identify intervals in a genome not covered by a query. 

Create flanking intervals from input intervals. 

Merge overlapping intervals. 

Partition intervals into elemental intervals 

Increase the size of input intervals. 

Adjust intervals by a fixed size. 

Sort a set of intervals. 

Multiple set operations 

Identify closest intervals. 

Compute coverage of intervals. 

Identify intersecting intervals. 

Calculate summaries from overlapping intervals. 

Subtract two sets of intervals. 

Identify intervals within a specified distance. 

Randomizing intervals 

Generate randomly placed intervals on a genome. 

Shuffle input intervals. 

Interval statistics 

Compute absolute distances between intervals. 

Compute relative distances between intervals. 

Fisher's test to measure overlap between two sets of intervals. 

Calculate the Jaccard statistic for two sets of intervals. 

Projection test for query interval overlap. 

Utilities 

Create intron features. 

Create transcription start site features. 

Create 3' UTR features. 

Create 5' UTR features. 

Divide intervals into new subintervals ("windows"). 

Convert BED12 to individual exons in BED6. 

Create example glyphs for valr functions. 

Select intervals bounded by a genome. 

Flip strands in intervals. 

Calculate interval spacing. 

Provide working directory for valr example files. 