Package: plyinteractions 1.5.0

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:Jacques Serizay [aut, cre]

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plyinteractions.pdf |plyinteractions.html✨
plyinteractions/json (API)
NEWS

# Install 'plyinteractions' in R:
install.packages('plyinteractions', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/js2264/plyinteractions/issues

Datasets:

    On BioConductor:plyinteractions-1.5.0(bioc 3.21)plyinteractions-1.4.0(bioc 3.20)

    softwareinfrastructure

    4.75 score 14 scripts 144 downloads 74 exports 67 dependencies

    Last updated 2 months agofrom:ac2f117c8d. Checks:OK: 1 NOTE: 6. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKDec 18 2024
    R-4.5-winNOTEDec 18 2024
    R-4.5-linuxNOTEDec 18 2024
    R-4.4-winNOTEDec 18 2024
    R-4.4-macNOTEDec 18 2024
    R-4.3-winNOTEDec 18 2024
    R-4.3-macNOTEDec 18 2024

    Exports:add_pairdistanchoranchor_3panchor_5panchor_centeranchor_endanchor_startanchors1anchors2annotateannotate_directedarrangeas_ginteractionscountcount_overlapscount_overlaps_directedend1end2filterfilter_by_non_overlapsfilter_by_overlapsfind_overlapsfind_overlaps_directedflank_downstreamflank_leftflank_rightflank_upstreamgroup_bygroup_datagroup_indicesgroup_keysgroup_rowsgroup_sizegroup_varsgroupsjoin_overlap_leftjoin_overlap_left_directedmutaten_groupspair_grangespinpin_anchors1pin_anchors2pin_bypin_firstpin_secondpinned_anchorsranges1ranges2renamereplace_anchorsselectseqnames1seqnames2shift_downstreamshift_leftshift_rightshift_upstreamslicestart1start2strand1strand2stretchsummarisesummarizetallyunanchorungroupunpinwidth1width2write_bedpewrite_pairs

    Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsclicodetoolscpp11crayoncurlDelayedArraydplyrfansiformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehttrInteractionSetIRangesjsonlitelambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrangesR6RcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrswithrXMLXVectoryamlzlibbioc

    Hi-C arithmetic with plyinteractions

    Rendered fromprocess_pairs.Rmdusingknitr::rmarkdownon Dec 18 2024.

    Last update: 2023-10-09
    Started: 2023-09-29

    plyinteractions

    Rendered fromplyinteractions.Rmdusingknitr::rmarkdownon Dec 18 2024.

    Last update: 2023-10-09
    Started: 2023-08-31

    Readme and manuals

    Help Manual

    Help pageTopics
    plyinteractions: a grammar of data manipulation for genomic interactionsplyinteractions-package plyinteractions
    Appends distance between interaction anchorsadd_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 GInteractionsannotate 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.frameas_ginteractions
    Arrange a GInteractions by a columnarrange.GInteractions dplyr-arrange
    Count or tally GInteractions per groupcount.GInteractions count.GroupedGInteractions dplyr-count tally.GroupedGInteractions
    Subset a GInteractions with tidyverse-like 'filter'dplyr-filter filter.GInteractions
    Group GInteractions by columnsdplyr-group_by group_by.DelegatingGInteractions group_by.GInteractions ungroup.GroupedGInteractions
    Mutate columns from a GInteractions objectdplyr-mutate mutate.GInteractions
    Rename columns from a GInteractions with tidyverse-like 'rename'dplyr-rename rename.GInteractions
    Select columns within GInteractions metadata columnsdplyr-select select.GInteractions
    Slice a GInteractions rows by their indexdplyr-slice slice.GInteractions
    Summarize GInteractions per groupdplyr-summarise dplyr-summarize summarise.GroupedGInteractions summarize.GroupedGInteractions
    Manage GInteractions anchors with plyrangesanchor.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 GRangescount_overlaps.GInteractions count_overlaps.PinnedGInteractions count_overlaps_directed.GInteractions count_overlaps_directed.PinnedGInteractions ginteractions-count-overlaps
    Export GInteractions as 'bedpe' or 'pairs' filesginteractions-export write_bedpe write_pairs
    Filter GInteractions overlapping with a GRangesfilter_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 GRangesfind_overlaps.GInteractions find_overlaps.PinnedGInteractions find_overlaps_directed.GInteractions find_overlaps_directed.PinnedGInteractions ginteractions-find-overlaps
    Join overlaps between a query GInteractions and a GRangesginteractions-join-overlap-left join_overlap_left.GInteractions join_overlap_left.PinnedGInteractions join_overlap_left_directed.GInteractions join_overlap_left_directed.PinnedGInteractions
    GInteractions grouping metadatagroup-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 objectpair_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
    Generate flanking regions from pinned anchors of a GInteractions object with plyrangesflank_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 plyranges-flank
    Shift pinned anchors of a GInteractions object with plyrangesplyranges-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 plyrangesplyranges-stretch stretch.AnchoredPinnedGInteractions stretch.PinnedGInteractions
    Replace anchors of a GInteractionsreplace_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