GenomicRanges

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.title[
# GenomicRanges
]
.author[
### Mikhail Dozmorov
]
.institute[
### Virginia Commonwealth University
]
.date[
### 2026-03-16
]

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## Ranges overview

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## Ranges in Bioconductor: IRanges and GRanges

Bioconductor utilizes a hierarchical range infrastructure to manage genomic intervals efficiently, moving from simple integer math to complex genomic coordinates.

`IRanges` (Integer Ranges)

The fundamental building block for interval algebra in R. It focuses strictly on the sequence of integers without biological context.
* **Core Components:** Defined by any two of `start`, `end`, and `width`.
* **Properties:**
    * **List-like Behavior:** Supports standard R operations like `length()`, subsetting `[]`, and `c()`.
    * **Metadata (`mcols`):** Allows you to attach any amount of data (e.g., p-values, scores) to each specific range.

* **Primary Use:** Non-genomic intervals or internal calculations where strand and chromosome are irrelevant.

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## Ranges in Bioconductor: IRanges and GRanges

Bioconductor utilizes a hierarchical range infrastructure to manage genomic intervals efficiently, moving from simple integer math to complex genomic coordinates.

`GRanges` (Genomic Ranges)

Extends `IRanges` by placing intervals onto a biological map. This is the "workhorse" class for most Bioconductor analyses.

* **The "Genomic" Context:** 
* `seqnames`: The chromosome or scaffold name (e.g., "chr1").
* `start`, `end`: Genomic coordinates
* `strand`: Defines the directionality (`+`, `-`, or `*` for unstranded).

.small[ **Key Methods:** `start(gr)`, `end(gr)`, `width(gr)`, `seqnames(gr)`, `strand(gr)`, and `mcols(gr)` ]

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## Ranges in Bioconductor: IRanges and GRanges

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## Ranges in Bioconductor: IRanges and GRanges

**`Seqinfo`:** A critical metadata component that tracks:

* **Genome Build:** (e.g., "hg38").

* **Sequence Lengths:** Ensures ranges do not accidentally exceed chromosome boundaries.

* **Circular Flags:** Identifies circular DNA (like mitochondria).

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## Range methods

* **Intra-range**: `shift()`, `narrow()`, `flank()`, `promoters()`, `resize()`

* **Inter-range**: `range()`, `reduce()`, `gaps()`, `disjoin()`, `coverage()`

* **Between-range**: `findOverlaps()`, `countOverlaps()`, `summarizeOverlaps()`, `%over%`, `union()`, `intersect()`

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## Lists of Genomic Ranges

* Useful for elements of the same type (e.g., exons within transcripts).

* Common trick: apply vectorized functions to unlisted representation, then re-list.