Package index • plyranges

About plyranges

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

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

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

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
pull(<Ranges>): Extract a single column from a Ranges object as a vector
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

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

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

pair_overlaps() pair_nearest() pair_precede() pair_follow(): Pair together two ranges objects

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

genome_info() set_genome_info() get_genome_info(): Construct annotation information

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

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
`%>%`: Pipe operator