# A fluent interface for manipulating GenomicRanges

## Documentation for package ‘plyranges’ version 1.20.0

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

## Help Pages

A B C D E F G I J M N O P R S T U W misc

plyranges-package | plyranges: a grammar of genomic data manipulation

## -- A --

add_nearest_distance | Add distance to nearest neighbours between two Ranges objects
add_nearest_distance_downstream | Add distance to nearest neighbours between two Ranges objects
add_nearest_distance_left | Add distance to nearest neighbours between two Ranges objects
add_nearest_distance_right | Add distance to nearest neighbours between two Ranges objects
add_nearest_distance_upstream | Add distance to nearest neighbours between two Ranges objects
anchor | Anchored Ranges objects
anchor_3p | Anchored Ranges objects
anchor_5p | Anchored Ranges objects
anchor_center | Anchored Ranges objects
anchor_centre | Anchored Ranges objects
anchor_end | Anchored Ranges objects
anchor_start | Anchored Ranges objects
arrange.Ranges | Sort a Ranges object
as_granges | Construct a I/GRanges object from a tibble or data.frame
as_iranges | Construct a I/GRanges object from a tibble or data.frame
as_ranges | Coerce an Rle or RleList object to Ranges

## -- B --

BamFileOperator-class | An abstract class to represent operations performed over a file
between | Row-wise set operations on Ranges objects
bind_ranges | Combine Ranges by concatentating them together

## -- C --

chop_by_gaps | Group a GRanges object by introns or gaps
chop_by_introns | Group a GRanges object by introns or gaps
complement_ranges | Vector-wise Range set-operations
complement_ranges_directed | Vector-wise Range set-operations
compute_coverage | Compute coverage over a Ranges object
count_overlaps | Count the number of overlaps between two Ranges objects
count_overlaps.GenomicRanges | Count the number of overlaps between two Ranges objects
count_overlaps.IntegerRanges | Count the number of overlaps between two Ranges objects
count_overlaps_directed | Count the number of overlaps between two Ranges objects
count_overlaps_directed.GenomicRanges | Count the number of overlaps between two Ranges objects
count_overlaps_within | Count the number of overlaps between two Ranges objects
count_overlaps_within.GenomicRanges | Count the number of overlaps between two Ranges objects
count_overlaps_within.IntegerRanges | Count the number of overlaps between two Ranges objects
count_overlaps_within_directed | Count the number of overlaps between two Ranges objects
count_overlaps_within_directed.GenomicRanges | Count the number of overlaps between two Ranges objects

## -- D --

DeferredGenomicRanges-class | DeferredGenomiRanges objects
disjoin_ranges | Disjoin then aggregate a Ranges object
disjoin_ranges_directed | Disjoin then aggregate a Ranges object

## -- E --

expand_ranges | Expand list-columns in a Ranges object

## -- F --

FileOperator-class | An abstract class to represent operations performed over a file
filter-ranges | Subset a 'Ranges' object
filter.Ranges | Subset a 'Ranges' object
filter_by_non_overlaps | Filter by overlapping/non-overlapping ranges
filter_by_overlaps | Filter by overlapping/non-overlapping ranges
find_overlaps | Find overlap between two Ranges
find_overlaps.GenomicRanges | Find overlap between two Ranges
find_overlaps.IntegerRanges | Find overlap between two Ranges
find_overlaps_directed | Find overlap between two Ranges
find_overlaps_directed.GenomicRanges | Find overlap between two Ranges
find_overlaps_within | Find overlap between two Ranges
find_overlaps_within.GenomicRanges | Find overlap between two Ranges
find_overlaps_within.IntegerRanges | Find overlap between two Ranges
find_overlaps_within_directed | Find overlap between two Ranges
find_overlaps_within_directed.GenomicRanges | Find overlap between two Ranges
flank_downstream | Generate flanking regions
flank_left | Generate flanking regions
flank_right | Generate flanking regions
flank_upstream | Generate flanking regions

## -- G --

genome_info | Construct annotation information
get_genome_info | Construct annotation information
GroupedGenomicRanges-class | Group a Ranges by one or more variables
GroupedIntegerRanges-class | Group a Ranges by one or more variables
groups.GroupedGenomicRanges | Group a Ranges by one or more variables
groups.GroupedIntegerRanges | Group a Ranges by one or more variables
group_by-ranges | Group a Ranges by one or more variables
group_by.GenomicRanges | Group a Ranges by one or more variables
group_by_overlaps | Find overlap between two Ranges
group_by_overlaps.GenomicRanges | Find overlap between two Ranges
group_by_overlaps.IntegerRanges | Find overlap between two Ranges

## -- I --

id_to_column | Tools for working with named Ranges
intersect_ranges | Vector-wise Range set-operations
intersect_ranges_directed | Vector-wise Range set-operations
interweave | Interweave a pair of Ranges objects together

## -- J --

join_follow | Find following Ranges
join_follow_left | Find following Ranges
join_follow_upstream | Find following Ranges
join_nearest | Find nearest neighbours between two Ranges objects
join_nearest_downstream | Find nearest neighbours between two Ranges objects
join_nearest_left | Find nearest neighbours between two Ranges objects
join_nearest_right | Find nearest neighbours between two Ranges objects
join_nearest_upstream | Find nearest neighbours between two Ranges objects
join_overlap_inner | Join by overlapping Ranges
join_overlap_inner_directed | Join by overlapping Ranges
join_overlap_inner_within | Join by overlapping Ranges
join_overlap_inner_within_directed | Join by overlapping Ranges
join_overlap_intersect | Join by overlapping Ranges
join_overlap_intersect_directed | Join by overlapping Ranges
join_overlap_intersect_within | Join by overlapping Ranges
join_overlap_intersect_within_directed | Join by overlapping Ranges
join_overlap_left | Join by overlapping Ranges
join_overlap_left_directed | Join by overlapping Ranges
join_overlap_left_within | Join by overlapping Ranges
join_overlap_left_within_directed | Join by overlapping Ranges
join_overlap_self | Find overlaps within a Ranges object
join_overlap_self_directed | Find overlaps within a Ranges object
join_overlap_self_within | Find overlaps within a Ranges object
join_overlap_self_within_directed | Find overlaps within a Ranges object
join_precede | Find preceding Ranges
join_precede_downstream | Find preceding Ranges
join_precede_right | Find preceding Ranges

## -- M --

mutate.Ranges | Modify a Ranges object

## -- N --

n | Compute the number of ranges in each group.
names_to_column | Tools for working with named Ranges
n_distinct | Compute the number of distinct unique values in a vector or List

## -- O --

overscope_ranges | Create an overscoped environment from a Ranges object

## -- P --

pair_follow | Pair together two ranges objects
pair_nearest | Pair together two ranges objects
pair_overlaps | Pair together two ranges objects
pair_precede | Pair together two ranges objects
plyranges | plyranges: a grammar of genomic data manipulation

## -- R --

ranges-info | Construct annotation information
read_bam | Read a BAM file
read_bed | Read a BED or BEDGraph file
read_bed_graph | Read a BED or BEDGraph file
read_bigwig | Read a BigWig file
read_gff | Read a GFF/GTF/GVT file
read_gff1 | Read a GFF/GTF/GVT file
read_gff2 | Read a GFF/GTF/GVT file
read_gff3 | Read a GFF/GTF/GVT file
read_narrowpeaks | Read a BED or BEDGraph file
read_wig | Read a WIG file
reduce_ranges | Reduce then aggregate a Ranges object
reduce_ranges_directed | Reduce then aggregate a Ranges object
remove_names | Tools for working with named Ranges

## -- S --

select.Ranges | Select metadata columns of the Ranges object by name or position
setdiff_ranges | Vector-wise Range set-operations
setdiff_ranges_directed | Vector-wise Range set-operations
set_end | Functional setters for Ranges objects
set_genome_info | Construct annotation information
set_seqnames | Functional setters for Ranges objects
set_start | Functional setters for Ranges objects
set_strand | Functional setters for Ranges objects
set_width | Functional setters for Ranges objects
shift_downstream | Shift all coordinates in a genomic interval left or right, upstream or downstream
shift_left | Shift all coordinates in a genomic interval left or right, upstream or downstream
shift_right | Shift all coordinates in a genomic interval left or right, upstream or downstream
shift_upstream | Shift all coordinates in a genomic interval left or right, upstream or downstream
slice.GroupedGenomicRanges | Choose rows by their position
slice.GroupedIntegerRanges | Choose rows by their position
slice.Ranges | Choose rows by their position
slide_ranges | Slide or tile over a Ranges object
span | Row-wise set operations on Ranges objects
stretch | Stretch a genomic interval
summarise.Ranges | Reduce multiple values in a Ranges down to a single value

## -- T --

tile_ranges | Slide or tile over a Ranges object

## -- U --

unanchor | Anchored Ranges objects
ungroup.GroupedGenomicRanges | Group a Ranges by one or more variables
union_ranges | Vector-wise Range set-operations
union_ranges_directed | Vector-wise Range set-operations

## -- W --

write_bed | Write a BED or BEDGraph file
write_bed_graph | Write a BED or BEDGraph file
write_bigwig | Write a BigWig file
write_gff | Write a GFF(123) file
write_gff1 | Write a GFF(123) file
write_gff2 | Write a GFF(123) file
write_gff3 | Write a GFF(123) file
write_narrowpeaks | Write a BED or BEDGraph file
write_wig | Write a WIG file

## -- misc --

%intersect% | Row-wise set operations on Ranges objects
%setdiff% | Row-wise set operations on Ranges objects
%union% | Row-wise set operations on Ranges objects