Genome Interval Arithmetic

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Documentation for package ‘valr’ version 0.8.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

valr-package	valr: genome interval arithmetic in R
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_bigwig	Import and convert a bigwig file into a valr compatible tbl
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.