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IRanges (version 2.6.0)

Infrastructure for manipulating intervals on sequences

Description

The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially (formally defined as Vector objects), as well as views on these Vector objects. Efficient list-like classes are also provided for storing big collections of instances of the basic classes. All classes in the package use consistent naming and share the same rich and consistent "Vector API" as much as possible.

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Version

Version

2.6.0

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in IRanges (2.6.0)

DataFrame-utils

Common operations on DataFrame objects
Views-class

Views objects
Ranges-class

Ranges objects
CompressedHitsList-class

CompressedHitsList objects
RangedSelection-class

Selection of ranges and columns
RangesList-class

List of Ranges
Rle-class-leftovers

Rle objects (old man page)
Vector-class-leftovers

Vector objects (old man page)
AtomicList

Lists of Atomic Vectors in Natural and Rle Form
Ranges-comparison

Comparing and ordering ranges
IRanges-constructor

The IRanges constructor and supporting functions
GappedRanges-class

GappedRanges objects
coverage-methods

Coverage of a set of ranges
read.Mask

Read a mask from a file
multisplit

Split elements belonging to multiple groups
findOverlaps-methods

Finding overlapping ranges
inter-range-methods

Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
intra-range-methods

Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
DataFrameList-class

List of DataFrames
seqapply

2 methods that should be documented somewhere else
AtomicList-utils

Common operations on AtomicList objects
IRanges internals

IRanges internals
NCList-class

Nested Containment List objects
IRangesList-class

List of IRanges and NormalIRanges
ViewsList-class

List of Views
nearest-methods

Finding the nearest range neighbor
reverse

reverse
IRanges-utils

IRanges utility functions
MaskCollection-class

MaskCollection objects
RleViews-class

The RleViews class
RangedDataList-class

Lists of RangedData
CompressedList-class

CompressedList objects
IRanges-class

IRanges and NormalIRanges objects
RangedData-class

Data on ranges
RleViewsList-class

List of RleViews
rdapply

Applying over spaces
List-class-leftovers

List objects (old man page)
Grouping-class

Grouping objects
Hits-class-leftovers

Examples of basic manipulation of Hits objects
extractList

Group elements of a vector-like object into a list-like object
setops-methods

Set operations on Ranges and RangesList objects
slice-methods

Slice a vector-like or list-like object
view-summarization-methods

Summarize views on a vector-like object with numeric values