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IRanges (version 2.6.1)

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

2.6.1

License

Artistic-2.0

Last Published

February 15th, 2017

Functions in IRanges (2.6.1)

coverage-methods

Coverage of a set of ranges
Views-class

Views objects
DataFrame-utils

Common operations on DataFrame objects
view-summarization-methods

Summarize views on a vector-like object with numeric values
CompressedHitsList-class

CompressedHitsList objects
CompressedList-class

CompressedList objects
Grouping-class

Grouping objects
Hits-class-leftovers

Examples of basic manipulation of Hits objects
RangedSelection-class

Selection of ranges and columns
Ranges-class

Ranges objects
DataFrameList-class

List of DataFrames
AtomicList-utils

Common operations on AtomicList objects
AtomicList

Lists of Atomic Vectors in Natural and Rle Form
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
MaskCollection-class

MaskCollection objects
multisplit

Split elements belonging to multiple groups
slice-methods

Slice a vector-like or list-like object
Vector-class-leftovers

Vector objects (old man page)
RleViews-class

The RleViews class
RleViewsList-class

List of RleViews
extractList

Group elements of a vector-like object into a list-like object
IRangesList-class

List of IRanges and NormalIRanges
List-class-leftovers

List objects (old man page)
RangesList-class

List of Ranges
Ranges-comparison

Comparing and ordering ranges
rdapply

Applying over spaces
read.Mask

Read a mask from a file
findOverlaps-methods

Finding overlapping ranges
GappedRanges-class

GappedRanges objects
IRanges internals

IRanges internals
NCList-class

Nested Containment List objects
IRanges-utils

IRanges utility functions
nearest-methods

Finding the nearest range neighbor
reverse

reverse
Rle-class-leftovers

Rle objects (old man page)
ViewsList-class

List of Views
IRanges-class

IRanges and NormalIRanges objects
IRanges-constructor

The IRanges constructor and supporting functions
RangedDataList-class

Lists of RangedData
RangedData-class

Data on ranges
seqapply

2 methods that should be documented somewhere else
setops-methods

Set operations on Ranges and RangesList objects