Package: plyinteractions 1.11.0
Jacques Serizay
plyinteractions: Extending tidy verbs to genomic interactions
Operate on `GInteractions` objects as tabular data using `dplyr`-like verbs. The functions and methods in `plyinteractions` provide a grammatical approach to manipulate `GInteractions`, to facilitate their integration in genomic analysis workflows.
Authors:
plyinteractions_1.11.0.tar.gz
plyinteractions_1.11.0.zip(r-4.7)plyinteractions_1.11.0.zip(r-4.6)plyinteractions_1.11.0.zip(r-4.5)
plyinteractions_1.11.0.tgz(r-4.6-any)plyinteractions_1.11.0.tgz(r-4.5-any)
plyinteractions_1.11.0.tar.gz(r-4.7-any)plyinteractions_1.11.0.tar.gz(r-4.6-any)
plyinteractions_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
plyinteractions/json (API)
NEWS
| # Install 'plyinteractions' in R: |
| install.packages('plyinteractions', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/js2264/plyinteractions/issues
- ce10_ARCC - Data files provided in the plyinteractions package
- ce10_REs - Data files provided in the plyinteractions package
- GM12878_HiCCUPS - Data files provided in the plyinteractions package
On BioConductor:plyinteractions-1.11.0(bioc 3.24)plyinteractions-1.10.0(bioc 3.23)
Last updated from:1f6d7487bf. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 291 | ||
| linux-devel-x86_64 | WARNING | 500 | ||
| source / vignettes | OK | 512 | ||
| linux-release-x86_64 | WARNING | 468 | ||
| macos-release-arm64 | WARNING | 389 | ||
| macos-oldrel-arm64 | WARNING | 315 | ||
| windows-devel | WARNING | 503 | ||
| windows-release | WARNING | 621 | ||
| windows-oldrel | WARNING | 504 | ||
| wasm-release | OK | 234 |
Exports:add_pairdistanchors1anchors2annotateannotate_directedas_ginteractionsend1end2flank_downstreamflank_leftflank_rightflank_upstreampair_grangespinpin_anchors1pin_anchors2pin_bypin_firstpin_secondpinned_anchorsranges1ranges2replace_anchorsseqnames1seqnames2shift_downstreamshift_leftshift_rightshift_upstreamshowstart1start2strand1strand2unpinwidth1width2write_bedpewrite_pairs
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurlDelayedArraydplyrformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrInteractionSetIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrangesR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectutf8vctrswithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Appends distance between interaction anchors | add_pairdist |
| Enhanced GInteractions getters | $,GInteractions-method anchors1 anchors1,GInteractions-method anchors2 anchors2,GInteractions-method end1 end1,GInteractions-method end2 end2,GInteractions-method ginteractions-getters ranges1 ranges1,GInteractions-method ranges2 ranges2,GInteractions-method seqnames1 seqnames1,GInteractions-method seqnames2 seqnames2,GInteractions-method start1 start1,GInteractions-method start2 start2,GInteractions-method strand1 strand1,GInteractions-method strand2 strand2,GInteractions-method width1 width1,GInteractions-method width2 width2,GInteractions-method |
| Annotate both anchors of a GInteractions | annotate annotate,GInteractions,GRanges,character-method annotate_directed annotate_directed,GInteractions,GRanges,character-method ginteractions-annotate |
| Construct a GInteractions object from a tibble, DataFrame or data.frame | as_ginteractions |
| Arrange a GInteractions by a column | arrange.GInteractions dplyr-arrange |
| Count or tally GInteractions per group | count.GInteractions count.GroupedGInteractions dplyr-count tally.GroupedGInteractions |
| Subset a GInteractions with tidyverse-like 'filter' | dplyr-filter filter.GInteractions |
| Group GInteractions by columns | dplyr-group_by group_by.DelegatingGInteractions group_by.GInteractions ungroup.GroupedGInteractions |
| Mutate columns from a GInteractions object | dplyr-mutate mutate.GInteractions |
| Rename columns from a GInteractions with tidyverse-like 'rename' | dplyr-rename rename.GInteractions |
| Select columns within GInteractions metadata columns | dplyr-select select.GInteractions |
| Slice a GInteractions rows by their index | dplyr-slice slice.GInteractions |
| Summarize GInteractions per group | dplyr-summarise dplyr-summarize summarise.GroupedGInteractions summarize.GroupedGInteractions |
| Manage GInteractions anchors with plyranges | anchor.AnchoredPinnedGInteractions anchor_3p.AnchoredPinnedGInteractions anchor_3p.PinnedGInteractions anchor_5p.AnchoredPinnedGInteractions anchor_5p.PinnedGInteractions anchor_center.AnchoredPinnedGInteractions anchor_center.PinnedGInteractions anchor_end.AnchoredPinnedGInteractions anchor_end.PinnedGInteractions anchor_start.AnchoredPinnedGInteractions anchor_start.PinnedGInteractions ginteractions-anchor unanchor.AnchoredPinnedGInteractions |
| Count overlaps between a query GInteractions and a GRanges | count_overlaps.GInteractions count_overlaps.PinnedGInteractions count_overlaps_directed.GInteractions count_overlaps_directed.PinnedGInteractions ginteractions-count-overlaps |
| Export GInteractions as 'bedpe' or 'pairs' files | ginteractions-export write_bedpe write_pairs |
| Filter GInteractions overlapping with a GRanges | filter_by_non_overlaps.GInteractions filter_by_non_overlaps.PinnedGInteractions filter_by_overlaps.GInteractions filter_by_overlaps.PinnedGInteractions ginteractions-filter-overlaps |
| Find overlaps between a query GInteractions and a GRanges | find_overlaps.GInteractions find_overlaps.PinnedGInteractions find_overlaps_directed.GInteractions find_overlaps_directed.PinnedGInteractions ginteractions-find-overlaps |
| Join overlaps between a query GInteractions and a GRanges | ginteractions-join-overlap-left join_overlap_left.GInteractions join_overlap_left.PinnedGInteractions join_overlap_left_directed.GInteractions join_overlap_left_directed.PinnedGInteractions |
| GInteractions grouping metadata | group-group_data groups.GroupedGInteractions group_data.GroupedGInteractions group_indices.GroupedGInteractions group_keys.GroupedGInteractions group_size.GroupedGInteractions group_vars.GInteractions group_vars.GroupedGInteractions n_groups.GroupedGInteractions |
| Pairwise combination of a GRanges object | pair_granges |
| Pin GInteractions by anchors set (anchors1 or anchors2). | ginteractions-pin pin pin,AnchoredPinnedGInteractions,character-method pin,AnchoredPinnedGInteractions,numeric-method pin,GInteractions,character-method pin,GInteractions,numeric-method pin,GroupedGInteractions,character-method pin,GroupedGInteractions,numeric-method pin,PinnedGInteractions,character-method pin,PinnedGInteractions,missing-method pin,PinnedGInteractions,numeric-method pinned_anchors pinned_anchors,AnchoredPinnedGInteractions-method pinned_anchors,PinnedGInteractions-method pin_anchors1 pin_anchors2 pin_by pin_first pin_second unpin unpin,AnchoredPinnedGInteractions-method unpin,GInteractions-method unpin,PinnedGInteractions-method |
| Data files provided in the plyinteractions package | ce10_ARCC ce10_REs GM12878_HiCCUPS plyinteractions-data |
| Generate flanking regions from pinned anchors of a GInteractions object | flank_downstream flank_downstream.PinnedGInteractions flank_downstream.Ranges flank_left flank_left.PinnedGInteractions flank_left.Ranges flank_right flank_right.PinnedGInteractions flank_right.Ranges flank_upstream flank_upstream.PinnedGInteractions flank_upstream.Ranges plyinteractions-flank |
| Shift pinned anchors of a GInteractions object with plyinteractions | plyinteractions-shift shift_downstream shift_downstream.PinnedGInteractions shift_downstream.Ranges shift_left shift_left.PinnedGInteractions shift_left.Ranges shift_right shift_right.PinnedGInteractions shift_right.Ranges shift_upstream shift_upstream.PinnedGInteractions shift_upstream.Ranges |
| Stretch pinned anchors of a GInteractions object with plyranges | plyranges-stretch stretch.AnchoredPinnedGInteractions stretch.PinnedGInteractions |
| Replace anchors of a GInteractions | replace_anchors replace_anchors,AnchoredPinnedGInteractions,missing,GRanges-method replace_anchors,AnchoredPinnedGInteractions,numeric,GRanges-method replace_anchors,GInteractions,character,GenomicRanges-method replace_anchors,GInteractions,numeric,GenomicRanges-method replace_anchors,PinnedGInteractions,missing,GenomicRanges-method |
| show method for 'GInteractions' objects | show,AnchoredPinnedGInteractions-method show,GInteractions-method show,GroupedGInteractions-method show,PinnedGInteractions-method show-GInteractions |
