Function reference • valr

Data types

Load data

read_bed() read_bed12() read_bedgraph() read_narrowpeak() read_broadpeak(): Read BED and related files.

read_bigwig(): Import and convert a bigwig file into a valr compatible tbl

read_genome(): Read genome files.

read_gtf(): Import and convert a GTF/GFF file into a valr compatible bed tbl format

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_genomecov(): Calculate coverage across a genome

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.

gr_to_bed(): Convert Granges to bed tibble

interval_spacing(): Calculate interval spacing.

check_interval() check_genome(): Bed-like data.frame requirements for valr functions

valr-package valr: valr: genome interval arithmetic in R

valr_example(): Provide working directory for valr example files.