About 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

Core verbs

mutate(<Ranges>)

Modify a Ranges object

summarise(<Ranges>)

Aggregate a Ranges object

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 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

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

An abstract class to represent operations performed over a file

DeferredGenomicRanges-class

DeferredGenomiRanges objects

Utilities

n()

Compute the number of ranges in each group.

as_ranges()

Coerce an Rle or RleList object to Ranges

set_width() set_start() set_end() set_seqnames() set_strand()

Functional setters for Ranges objects

overscope_ranges()

Create an overscoped environment from a Ranges object

tbl_vars(<Ranges>) tbl_vars(<GenomicRanges>)

Re-exports Rexported functions from the tidyverse