Function reference • plyranges

About plyranges
`plyranges` `plyranges-package`	plyranges: a grammar of genomic data manipulation
Ranges
`as_iranges()` `as_granges()`	Construct a I/GRanges object from a tibble or data.frame
`interweave()`	Interweave a pair of Ranges objects together
`bind_ranges()`	Combine Ranges by concatentating them together
`tile_ranges()` `slide_ranges()`	Slide or tile over a Ranges object
Arithmetic
`anchor()` `unanchor()` `anchor_start()` `anchor_end()` `anchor_center()` `anchor_centre()` `anchor_3p()` `anchor_5p()`	Anchored Ranges objects
`stretch()`	Stretch a genomic interval
`shift_left()` `shift_right()` `shift_upstream()` `shift_downstream()`	Shift all coordinates in a genomic interval left or right, upstream or downstream
`flank_left()` `flank_right()` `flank_upstream()` `flank_downstream()`	Generate flanking regions
`chop_by_introns()` `chop_by_gaps()`	Group a GRanges object by introns or gaps
`n()`	Compute the number of ranges in each group.
`n_distinct()`	Compute the number of distinct unique values in a vector or List
Core verbs
`mutate(<Ranges>)`	Modify a Ranges object
`summarise(<Ranges>)`	Reduce multiple values in a Ranges down to a single value
`filter(<Ranges>)`	Subset a `Ranges` object
`arrange(<Ranges>)`	Sort a Ranges object
`select(<Ranges>)`	Select metadata columns of the Ranges object by name or position
`slice(<Ranges>)` `slice(<GroupedGenomicRanges>)` `slice(<GroupedIntegerRanges>)`	Choose rows by their position
`group_by(<GenomicRanges>)` `ungroup(<GroupedGenomicRanges>)` `groups(<GroupedGenomicRanges>)` `groups(<GroupedIntegerRanges>)`	Group a Ranges by one or more variables
`reduce_ranges()` `reduce_ranges_directed()`	Reduce then aggregate a Ranges object
`disjoin_ranges()` `disjoin_ranges_directed()`	Disjoin then aggregate a Ranges object
`compute_coverage()`	Compute coverage over a Ranges object
`expand_ranges()`	Expand list-columns in a Ranges object
Overlaps
`join_overlap_intersect()` `join_overlap_intersect_within()` `join_overlap_intersect_directed()` `join_overlap_intersect_within_directed()` `join_overlap_inner()` `join_overlap_inner_within()` `join_overlap_inner_directed()` `join_overlap_inner_within_directed()` `join_overlap_left()` `join_overlap_left_within()` `join_overlap_left_directed()` `join_overlap_left_within_directed()`	Join by overlapping Ranges
`join_overlap_self()` `join_overlap_self_within()` `join_overlap_self_directed()` `join_overlap_self_within_directed()`	Find overlaps within a Ranges object
`filter_by_overlaps()` `filter_by_non_overlaps()` `filter_by_overlaps_directed()` `filter_by_non_overlaps_directed()`	Filter by overlapping/non-overlapping ranges
`find_overlaps()` `find_overlaps_within()` `find_overlaps_directed()` `find_overlaps_within_directed()` `group_by_overlaps()`	Find overlap between two Ranges
`count_overlaps()` `count_overlaps_within()` `count_overlaps_directed()` `count_overlaps_within_directed()`	Count the number of overlaps between two Ranges objects
Nearest neighbours
`join_follow()` `join_follow_left()` `join_follow_upstream()`	Find following Ranges
`join_precede()` `join_precede_right()` `join_precede_downstream()`	Find preceding Ranges
`join_nearest()` `join_nearest_left()` `join_nearest_right()` `join_nearest_upstream()` `join_nearest_downstream()`	Find nearest neighbours between two Ranges objects
`add_nearest_distance()` `add_nearest_distance_left()` `add_nearest_distance_right()` `add_nearest_distance_upstream()` `add_nearest_distance_downstream()`	Add distance to nearest neighbours between two Ranges objects
Pairing up Ranges
`pair_overlaps()` `pair_nearest()` `pair_precede()` `pair_follow()`	Pair together two ranges objects
Set operations
`intersect_ranges()` `intersect_ranges_directed()` `union_ranges()` `union_ranges_directed()` `setdiff_ranges()` `setdiff_ranges_directed()` `complement_ranges()` `complement_ranges_directed()`	Vector-wise Range set-operations
`%union%` `%intersect%` `%setdiff%` `between()` `span()`	Row-wise set operations on Ranges objects
Annotation
`genome_info()` `set_genome_info()` `get_genome_info()`	Construct annotation information
Reading and Writing Genomics Data
`read_bam()`	Read a BAM file
`read_bed()` `read_bed_graph()` `read_narrowpeaks()`	Read a BED or BEDGraph file
`write_bed()` `write_bed_graph()` `write_narrowpeaks()`	Write a BED or BEDGraph file
`read_bigwig()`	Read a BigWig file
`write_bigwig()`	Write a BigWig file
`read_wig()`	Read a WIG file
`write_wig()`	Write a WIG file
`read_gff()` `read_gff1()` `read_gff2()` `read_gff3()`	Read a GFF/GTF/GVT file
`write_gff()` `write_gff1()` `write_gff2()` `write_gff3()`	Write a GFF(123) file
`FileOperator-class` `BamFileOperator-class`	An abstract class to represent operations performed over a file
`DeferredGenomicRanges-class`	DeferredGenomiRanges objects
Utilities
`remove_names()` `names_to_column()` `id_to_column()`	Tools for working with named Ranges
`set_width()` `set_start()` `set_end()` `set_seqnames()` `set_strand()`	Functional setters for Ranges objects
`as_ranges()`	Coerce an Rle or RleList object to Ranges
`overscope_ranges()`	Create an overscoped environment from a Ranges object
`reexports` `!!!` `!!` `%>%` `filter` `group_by` `groups` `ungroup` `group_vars` `mutate` `select` `summarise` `summarize` `arrange` `slice`	Objects exported from other packages.

Reference

About plyranges

Ranges

Arithmetic

Core verbs

Overlaps

Nearest neighbours

Pairing up Ranges

Set operations

Annotation

Reading and Writing Genomics Data

Utilities