plyinteractions

plyinteractions provides a consistent interface for importing genomic interactions from pairs and bedpe files into GInteractions objects in R and for manipulating them using a tidy grammar.

plyranges operates on genomic ranges (e.g. implemented as GRanges objects in Bioconductor) and introduces a tidy grammar for manipulating them. Genomic interactions (implemented as GInteractions objects in Bioconductor) are more complex than genomic ranges in that each observation (row) corresponds to a pair of two genomic ranges, each one with its own metadata. plyinteractions extends plyranges syntax to manipulate genomic interactions in R using dplyr verbs and tidy operations.

The grammar of tidy genomic data transformation defined in plyranges and available for GInteractions currently supports:

• dplyr verbs (for GInteractions and GroupedGInteractions):

  • Group genomic interactions with group_by;
  • Summarize grouped genomic interactions with summarize;
  • Tally/count grouped genomic interactions with tally and count;
  • Modify genomic interactions with mutate;
  • Subset genomic interactions with filter using <data-masking> and logical expressions;
  • Pick out any columns from the associated metadata with select using <tidy-select> arguments;
  • Subset using indices with slice;
  • Order genomic interactions with arrange using categorical/numerical variables.

• plyranges verbs (for PinnedGInteractions and AnchoredPinnedGInteractions):

  • Stretch specific anchors of genomic interactions to a given width with stretch;
  • anchor_* functions to control how stretching is performed;
  • Shift specific anchors of genomic interactions with shift;
  • Obtain flanking GRanges from specific anchors of genomic interactions with flank.

Note: In the genomic interaction field, the “anchor” term typically refers to the two genomic loci brought together into an interaction. In plyranges, the term anchor is used to specify which “part” of a genomic locus is fixed (e.g. “5p”, 3p”, “center”) and, incidently, which one can be modified by plyranges verbs.

For more details on GInteractions “anchors” vs. plyranges anchoring system, read this section from our vignette.

• Overlapping operations (for GInteractions and PinnedGInteractions):

  • find_overlaps
  • count_overlaps
  • filter_by_overlaps and filter_by_non_overlaps
  • join_overlap_left

Installation

plyinteractions can be currently be installed from GitHub:

BiocManager::install("tidyomics/plyinteractions")

Using plyinteractions

Read vignette("plyinteractions") for more details.

Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Acknowledgments

plyinteractions package is heavily based on plyranges. It adapts a number of functions and methods defined in that package, and would not have been developed without the seminal work from Stuart Lee, Dianne Cook and Michael Lawrence:

• Lee, Stuart, Dianne Cook, and Michael Lawrence. 2019. “Plyranges: A Grammar of Genomic Data Transformation.” Genome Biology 20 (1): 4. https://doi.org/10.1186/s13059-018-1597-8.

This package is largely inspired by the tidyverse:

• Wickham H, François R, Henry L, Müller K, Vaughan D (2023). dplyr: A Grammar of Data Manipulation. R package version 1.1.2, https://CRAN.R-project.org/package=dplyr.
• Henry L, Wickham H (2023). rlang: Functions for Base Types and Core R and ‘Tidyverse’ Features. R package version 1.1.1, https://CRAN.R-project.org/package=rlang.