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.