Man pages for valr
Genome Interval Arithmetic

bed12_to_exonsConvert BED12 to individual exons in BED6.
bed_absdistCompute absolute distances between intervals.
bed_closestIdentify closest intervals.
bed_clusterCluster neighboring intervals.
bed_complementIdentify intervals in a genome not covered by a query.
bed_coverageCompute coverage of intervals.
bed_fisherFisher's test to measure overlap between two sets of...
bed_flankCreate flanking intervals from input intervals.
bed_glyphCreate example glyphs for valr functions.
bed_intersectIdentify intersecting intervals.
bed_jaccardCalculate the Jaccard statistic for two sets of intervals.
bed_makewindowsDivide intervals into new sub-intervals ("windows").
bed_mapCalculate summaries from overlapping intervals.
bed_mergeMerge overlapping intervals.
bed_partitionPartition intervals into elemental intervals
bed_projectionProjection test for query interval overlap.
bed_randomGenerate randomly placed intervals on a genome.
bed_reldistCompute relative distances between intervals.
bed_shiftAdjust intervals by a fixed size.
bed_shuffleShuffle input intervals.
bed_slopIncrease the size of input intervals.
bed_sortSort a set of intervals.
bed_subtractSubtract two sets of intervals.
bed_windowIdentify intervals within a specified distance.
bound_intervalsSelect intervals bounded by a genome.
create_intronsCreate intron features.
create_tssCreate transcription start site features.
create_utrs3Create 3' UTR features.
create_utrs5Create 5' UTR features.
dbFetch data from remote databases.
flip_strandsFlip strands in intervals.
gr_to_bedConvert Granges to bed tibble
idPlyr function id packaged due to plyr being retired Compute a...
id_varPlyr function id_var packaged due to plyr being retired...
interval_spacingCalculate interval spacing.
ivl_dfBed-like data.frame requirements for valr functions
read_bedRead BED and related files.
read_bigwigImport and convert a bigwig file into a valr compatible tbl
read_genomeRead genome files.
read_gtfImport and convert a GTF/GFF file into a valr compatible bed...
read_vcfRead a VCF file.
valrvalr: genome interval arithmetic in R
valr_exampleProvide working directory for valr example files.
valr documentation built on Sept. 19, 2023, 1:07 a.m.