# Extending tidy verbs to genomic interactions

## Documentation for package ‘plyinteractions’ version 1.4.0

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

## Help Pages

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

plyinteractions-package | plyinteractions: a grammar of data manipulation for genomic interactions

## -- A --

add_pairdist | Appends distance between interaction anchors
anchor.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
anchors1 | Enhanced GInteractions getters
anchors1-method | Enhanced GInteractions getters
anchors2 | Enhanced GInteractions getters
anchors2-method | Enhanced GInteractions getters
anchor_3p.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_3p.PinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_5p.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_5p.PinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_center.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_center.PinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_end.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_end.PinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_start.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
anchor_start.PinnedGInteractions | Manage GInteractions anchors with plyranges
annotate | Annotate both anchors of a GInteractions
annotate-method | Annotate both anchors of a GInteractions
annotate_directed | Annotate both anchors of a GInteractions
annotate_directed-method | Annotate both anchors of a GInteractions
arrange.GInteractions | Arrange a GInteractions by a column
as_ginteractions | Construct a GInteractions object from a tibble, DataFrame or data.frame

## -- C --

count.GInteractions | Count or tally GInteractions per group
count.GroupedGInteractions | Count or tally GInteractions per group
count_overlaps.GInteractions | Count overlaps between a query GInteractions and a GRanges
count_overlaps.PinnedGInteractions | Count overlaps between a query GInteractions and a GRanges
count_overlaps_directed.GInteractions | Count overlaps between a query GInteractions and a GRanges
count_overlaps_directed.PinnedGInteractions | Count overlaps between a query GInteractions and a GRanges

## -- D --

dplyr-arrange | Arrange a GInteractions by a column
dplyr-count | Count or tally GInteractions per group
dplyr-filter | Subset a GInteractions with tidyverse-like 'filter'
dplyr-group_by | Group GInteractions by columns
dplyr-mutate | Mutate columns from a GInteractions object
dplyr-rename | Rename columns from a GInteractions with tidyverse-like 'rename'
dplyr-select | Select columns within GInteractions metadata columns
dplyr-slice | Slice a GInteractions rows by their index
dplyr-summarise | Summarize GInteractions per group
dplyr-summarize | Summarize GInteractions per group

## -- E --

end1 | Enhanced GInteractions getters
end1-method | Enhanced GInteractions getters
end2 | Enhanced GInteractions getters
end2-method | Enhanced GInteractions getters

## -- F --

filter.GInteractions | Subset a GInteractions with tidyverse-like 'filter'
filter_by_non_overlaps.GInteractions | Filter GInteractions overlapping with a GRanges
filter_by_non_overlaps.PinnedGInteractions | Filter GInteractions overlapping with a GRanges
filter_by_overlaps.GInteractions | Filter GInteractions overlapping with a GRanges
filter_by_overlaps.PinnedGInteractions | Filter GInteractions overlapping with a GRanges
find_overlaps.GInteractions | Find overlaps between a query GInteractions and a GRanges
find_overlaps.PinnedGInteractions | Find overlaps between a query GInteractions and a GRanges
find_overlaps_directed.GInteractions | Find overlaps between a query GInteractions and a GRanges
find_overlaps_directed.PinnedGInteractions | Find overlaps between a query GInteractions and a GRanges
flank_downstream | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_downstream.PinnedGInteractions | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_downstream.Ranges | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_left | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_left.PinnedGInteractions | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_left.Ranges | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_right | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_right.PinnedGInteractions | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_right.Ranges | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_upstream | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_upstream.PinnedGInteractions | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
flank_upstream.Ranges | Generate flanking regions from pinned anchors of a GInteractions object with plyranges

## -- G --

ginteractions-anchor | Manage GInteractions anchors with plyranges
ginteractions-annotate | Annotate both anchors of a GInteractions
ginteractions-count-overlaps | Count overlaps between a query GInteractions and a GRanges
ginteractions-export | Export GInteractions as 'bedpe' or 'pairs' files
ginteractions-filter-overlaps | Filter GInteractions overlapping with a GRanges
ginteractions-find-overlaps | Find overlaps between a query GInteractions and a GRanges
ginteractions-getters | Enhanced GInteractions getters
ginteractions-join-overlap-left | Join overlaps between a query GInteractions and a GRanges
ginteractions-pin | Pin GInteractions by anchors set (anchors1 or anchors2).
group-group_data | GInteractions grouping metadata
groups.GroupedGInteractions | GInteractions grouping metadata
group_by.DelegatingGInteractions | Group GInteractions by columns
group_by.GInteractions | Group GInteractions by columns
group_data.GroupedGInteractions | GInteractions grouping metadata
group_indices.GroupedGInteractions | GInteractions grouping metadata
group_keys.GroupedGInteractions | GInteractions grouping metadata
group_size.GroupedGInteractions | GInteractions grouping metadata
group_vars.GInteractions | GInteractions grouping metadata
group_vars.GroupedGInteractions | GInteractions grouping metadata

## -- J --

join_overlap_left.GInteractions | Join overlaps between a query GInteractions and a GRanges
join_overlap_left.PinnedGInteractions | Join overlaps between a query GInteractions and a GRanges
join_overlap_left_directed.GInteractions | Join overlaps between a query GInteractions and a GRanges
join_overlap_left_directed.PinnedGInteractions | Join overlaps between a query GInteractions and a GRanges

## -- M --

mutate.GInteractions | Mutate columns from a GInteractions object

## -- N --

n_groups.GroupedGInteractions | GInteractions grouping metadata

## -- P --

pair_granges | Pairwise combination of a GRanges object
pin | Pin GInteractions by anchors set (anchors1 or anchors2).
pin-method | Pin GInteractions by anchors set (anchors1 or anchors2).
pinned_anchors | Pin GInteractions by anchors set (anchors1 or anchors2).
pinned_anchors-method | Pin GInteractions by anchors set (anchors1 or anchors2).
pin_anchors1 | Pin GInteractions by anchors set (anchors1 or anchors2).
pin_anchors2 | Pin GInteractions by anchors set (anchors1 or anchors2).
pin_by | Pin GInteractions by anchors set (anchors1 or anchors2).
pin_first | Pin GInteractions by anchors set (anchors1 or anchors2).
pin_second | Pin GInteractions by anchors set (anchors1 or anchors2).
plyinteractions | plyinteractions: a grammar of data manipulation for genomic interactions
plyranges-flank | Generate flanking regions from pinned anchors of a GInteractions object with plyranges
plyranges-shift | Shift pinned anchors of a GInteractions object with plyranges
plyranges-stretch | Stretch pinned anchors of a GInteractions object with plyranges

## -- R --

ranges1 | Enhanced GInteractions getters
ranges1-method | Enhanced GInteractions getters
ranges2 | Enhanced GInteractions getters
ranges2-method | Enhanced GInteractions getters
rename.GInteractions | Rename columns from a GInteractions with tidyverse-like 'rename'
replace_anchors | Replace anchors of a GInteractions
replace_anchors-method | Replace anchors of a GInteractions

## -- S --

select.GInteractions | Select columns within GInteractions metadata columns
seqnames1 | Enhanced GInteractions getters
seqnames1-method | Enhanced GInteractions getters
seqnames2 | Enhanced GInteractions getters
seqnames2-method | Enhanced GInteractions getters
shift_downstream | Shift pinned anchors of a GInteractions object with plyranges
shift_downstream.PinnedGInteractions | Shift pinned anchors of a GInteractions object with plyranges
shift_downstream.Ranges | Shift pinned anchors of a GInteractions object with plyranges
shift_left | Shift pinned anchors of a GInteractions object with plyranges
shift_left.PinnedGInteractions | Shift pinned anchors of a GInteractions object with plyranges
shift_left.Ranges | Shift pinned anchors of a GInteractions object with plyranges
shift_right | Shift pinned anchors of a GInteractions object with plyranges
shift_right.PinnedGInteractions | Shift pinned anchors of a GInteractions object with plyranges
shift_right.Ranges | Shift pinned anchors of a GInteractions object with plyranges
shift_upstream | Shift pinned anchors of a GInteractions object with plyranges
shift_upstream.PinnedGInteractions | Shift pinned anchors of a GInteractions object with plyranges
shift_upstream.Ranges | Shift pinned anchors of a GInteractions object with plyranges
slice.GInteractions | Slice a GInteractions rows by their index
start1 | Enhanced GInteractions getters
start1-method | Enhanced GInteractions getters
start2 | Enhanced GInteractions getters
start2-method | Enhanced GInteractions getters
strand1 | Enhanced GInteractions getters
strand1-method | Enhanced GInteractions getters
strand2 | Enhanced GInteractions getters
strand2-method | Enhanced GInteractions getters
stretch.AnchoredPinnedGInteractions | Stretch pinned anchors of a GInteractions object with plyranges
stretch.PinnedGInteractions | Stretch pinned anchors of a GInteractions object with plyranges
summarise.GroupedGInteractions | Summarize GInteractions per group
summarize.GroupedGInteractions | Summarize GInteractions per group

## -- T --

tally.GroupedGInteractions | Count or tally GInteractions per group

## -- U --

unanchor.AnchoredPinnedGInteractions | Manage GInteractions anchors with plyranges
ungroup.GroupedGInteractions | Group GInteractions by columns
unpin | Pin GInteractions by anchors set (anchors1 or anchors2).
unpin-method | Pin GInteractions by anchors set (anchors1 or anchors2).

## -- W --

width1 | Enhanced GInteractions getters
width1-method | Enhanced GInteractions getters
width2 | Enhanced GInteractions getters
width2-method | Enhanced GInteractions getters
write_bedpe | Export GInteractions as 'bedpe' or 'pairs' files
write_pairs | Export GInteractions as 'bedpe' or 'pairs' files

## -- misc --

$-method | Enhanced GInteractions getters