R: Genome Interval Arithmetic

# Genome Interval Arithmetic

## Documentation for package ‘valr’ version 0.9.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

bed12_to_exons | Convert BED12 to individual exons in BED6.
bed_absdist | Compute absolute distances between intervals.
bed_closest | Identify closest intervals.
bed_cluster | Cluster neighboring intervals.
bed_complement | Identify intervals in a genome not covered by a query.
bed_coverage | Compute coverage of intervals.
bed_fisher | Fisher's test to measure overlap between two sets of intervals.
bed_flank | Create flanking intervals from input intervals.
bed_genomecov | Calculate coverage across a genome
bed_glyph | Create example glyphs for valr functions.
bed_intersect | Identify intersecting intervals.
bed_jaccard | Calculate the Jaccard statistic for two sets of intervals.
bed_makewindows | Divide intervals into new sub-intervals ("windows").
bed_map | Calculate summaries from overlapping intervals.
bed_merge | Merge overlapping intervals.
bed_partition | Partition intervals into elemental intervals
bed_projection | Projection test for query interval overlap.
bed_random | Generate randomly placed intervals on a genome.
bed_reldist | Compute relative distances between intervals.
bed_shift | Adjust intervals by a fixed size.
bed_shuffle | Shuffle input intervals.
bed_slop | Increase the size of input intervals.
bed_sort | Sort a set of intervals.
bed_subtract | Subtract two sets of intervals.
bed_window | Identify intervals within a specified distance.
bound_intervals | Select intervals bounded by a genome.
check_genome | Bed-like data.frame requirements for valr functions
check_interval | Bed-like data.frame requirements for valr functions
concat | Calculate summaries from overlapping intervals.
create_introns | Create intron features.
create_tss | Create transcription start site features.
create_utrs3 | Create 3' UTR features.
create_utrs5 | Create 5' UTR features.
db | Fetch data from remote databases.
db_ensembl | Fetch data from remote databases.
db_ucsc | Fetch data from remote databases.
flip_strands | Flip strands in intervals.
genome_df | Bed-like data.frame requirements for valr functions
gr_to_bed | Convert Granges to bed tibble
interval_spacing | Calculate interval spacing.
ivl_df | Bed-like data.frame requirements for valr functions
read_bed | Read BED and related files.
read_bed12 | Read BED and related files.
read_bedgraph | Read BED and related files.
read_broadpeak | Read BED and related files.
read_genome | Read genome files.
read_gtf | Import and convert a GTF/GFF file into a valr compatible bed tbl format
read_narrowpeak | Read BED and related files.
read_vcf | Read a VCF file.
valr | valr: genome interval arithmetic in R
valr_example | Provide working directory for valr example files.
values | Calculate summaries from overlapping intervals.
values_unique | Calculate summaries from overlapping intervals.