Man pages for rnabioco/valr
Genome Interval Arithmetic
| 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... |
| 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. |
| 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. |
| flip_strands | Flip strands in intervals. |
| gr_to_bed | Convert Granges to bed tibble |
| id | Plyr function id packaged due to plyr being retired Compute a... |
| id_var | Plyr function id_var packaged due to plyr being retired... |
| interval_spacing | Calculate interval spacing. |
| ivl_df | Bed-like data.frame requirements for valr functions |
| read_bed | 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... |
| read_vcf | Read a VCF file. |
| valr | valr: genome interval arithmetic in R |
| valr_example | Provide working directory for valr example files. |
