plyranges-package {plyranges} | R Documentation

## plyranges: a grammar of genomic data manipulation

### Description

plyranges is a dplyr like API to the Ranges/GenomicRanges infrastructure in Bioconductor.

### Details

plryanges provides a consistent interface for importing and wrangling genomics data from a variety of sources. The package defines a grammar of genomic data manipulation through a set of verbs. These verbs can be used to construct human readable analysis pipelines based on Ranges objects.

- Modify genomic regions with the `set_width()` and `stretch()` functions.

- Modify genomic regions while fixing the start/end/center coordinates with the `anchors()` family of functions.

- Sort genomic ranges with `arrange()`.

- Modify, subset, and aggregate genomic data with the `mutate()`, `filter()`, and `summarise()`functions.

- Any of the above operations can be performed on partitions of the data with `group_by()`.

- Find nearest neighbour genomic regions with the `join_nearest()` family of functions.

- Find overlaps between ranges with the `join_overlap_inner()` family of functions.

- Merge all overlapping and adjacent genomic regions with `reduce_ranges()`.

- Merge the end points of all genomic regions with `disjoin_ranges()`.

- Import and write common genomic data formats with the `read_/write_` family of functions.

For more details on the features of plryanges, read the vignette: `browseVignettes(package = "plyranges")`

### Author(s)

Maintainer: Stuart Lee lee.s@wehi.edu.au (ORCID)

Authors:

- Michael Lawrence [contributor]

- Dianne Cook [contributor]

Other contributors:

- Spencer Nystrom (ORCID) [contributor]

### See Also

Useful links:

- Report bugs at https://github.com/sa-lee/plyranges

[Package plyranges version 1.12.1 Index]