Package index • plyinteractions

About plyinteractions

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

Constructors

as_ginteractions(): Construct a GInteractions object from a tibble, DataFrame or data.frame

anchors1() anchors2() seqnames1() seqnames2() start1() start2() end1() end2() width1() width2() strand1() strand2() ranges1() ranges2() `$`(<GInteractions>): Enhanced GInteractions getters

pair_granges(): Pairwise combination of a GRanges object

`dplyr` core verbs

arrange(<GInteractions>): Arrange a GInteractions by a column

tally(<GroupedGInteractions>) count(<GroupedGInteractions>) count(<GInteractions>): Count or tally GInteractions per group

filter(<GInteractions>): Subset a GInteractions with tidyverse-like filter

group_by(<GInteractions>) group_by(<DelegatingGInteractions>) ungroup(<GroupedGInteractions>): Group GInteractions by columns

mutate(<GInteractions>): Mutate columns from a GInteractions object

rename(<GInteractions>): Rename columns from a GInteractions with tidyverse-like rename

select(<GInteractions>): Select columns within GInteractions metadata columns

slice(<GInteractions>): Slice a GInteractions rows by their index

summarise(<GroupedGInteractions>) summarize(<GroupedGInteractions>): Summarize GInteractions per group

`dplyr` group helpers

group_data(<GroupedGInteractions>) group_keys(<GroupedGInteractions>) group_indices(<GroupedGInteractions>) group_vars(<GInteractions>) group_vars(<GroupedGInteractions>) groups(<GroupedGInteractions>) group_size(<GroupedGInteractions>) n_groups(<GroupedGInteractions>): GInteractions grouping metadata

`plyranges` verbs

flank_downstream() flank_upstream() flank_right() flank_left(): Generate flanking regions from pinned anchors of a GInteractions object with plyranges

shift_downstream() shift_upstream() shift_right() shift_left(): Shift pinned anchors of a GInteractions object with plyranges

stretch(<AnchoredPinnedGInteractions>) stretch(<PinnedGInteractions>): Stretch pinned anchors of a GInteractions object with plyranges

Overlapping GInteractions

find_overlaps(<PinnedGInteractions>) find_overlaps(<GInteractions>) find_overlaps_directed(<PinnedGInteractions>) find_overlaps_directed(<GInteractions>): Find overlaps between a query GInteractions and a GRanges

count_overlaps(<PinnedGInteractions>) count_overlaps(<GInteractions>) count_overlaps_directed(<PinnedGInteractions>) count_overlaps_directed(<GInteractions>): Count overlaps between a query GInteractions and a GRanges

filter_by_overlaps(<PinnedGInteractions>) filter_by_overlaps(<GInteractions>) filter_by_non_overlaps(<PinnedGInteractions>) filter_by_non_overlaps(<GInteractions>): Filter GInteractions overlapping with a GRanges

join_overlap_left(<PinnedGInteractions>) join_overlap_left(<GInteractions>) join_overlap_left_directed(<PinnedGInteractions>) join_overlap_left_directed(<GInteractions>): Join overlaps between a query GInteractions and a GRanges

Enriching GInteractions

annotate() annotate_directed(): Annotate both anchors of a GInteractions

add_pairdist(): Appends distance between interaction anchors

Pinning GInteractions

pin() pin_by() pinned_anchors() unpin() pin_first() pin_second() pin_anchors1() pin_anchors2(): Pin GInteractions by anchors set (anchors1 or anchors2).

Anchoring GInteractions

anchor(<AnchoredPinnedGInteractions>) unanchor(<AnchoredPinnedGInteractions>) anchor_start(<PinnedGInteractions>) anchor_end(<PinnedGInteractions>) anchor_center(<PinnedGInteractions>) anchor_3p(<PinnedGInteractions>) anchor_5p(<PinnedGInteractions>) anchor_start(<AnchoredPinnedGInteractions>) anchor_end(<AnchoredPinnedGInteractions>) anchor_center(<AnchoredPinnedGInteractions>) anchor_3p(<AnchoredPinnedGInteractions>) anchor_5p(<AnchoredPinnedGInteractions>): Manage GInteractions anchors with plyranges

replace_anchors(): Replace anchors of a GInteractions

Exporting GInteractions

write_bedpe() write_pairs(): Export GInteractions as bedpe or pairs files