Extending tidy verbs to genomic interactions
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Documentation for package ‘plyinteractions’ version 1.5.0
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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 |