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IRanges (version 2.4.1)

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

2.4.1

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in IRanges (2.4.1)

coverage-methods

Coverage of a set of ranges
NCList-class

Nested Containment List objects
DataFrame-utils

Common operations on DataFrame objects
Hits-class-leftovers

Examples of basic manipulation of Hits objects
HitsList-class

List of Hits objects
multisplit

Split elements belonging to multiple groups
IRanges-class

IRanges and NormalIRanges objects
IRanges-constructor

The IRanges constructor and supporting functions
List-class-leftovers

List objects (old man page)
read.Mask

Read a mask from a file
IRangesList-class

List of IRanges and NormalIRanges
reverse

reverse
setops-methods

Set operations on IRanges and RangesList objects
slice-methods

Slice a vector-like or list-like object
extractList

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

Finding overlapping ranges
IntervalTree-class

Interval Search Trees
mapCoords-methods

Mapping of ranges to another sequence
intra-range-methods

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

List of RleViews
MaskCollection-class

MaskCollection objects
updateObject-methods

Update an object of a class defined in the IRanges package to its current class definition
seqapply

2 methods that should be documented somewhere else
Vector-class-leftovers

Vector objects (old man page)
GappedRanges-class

GappedRanges objects
Grouping-class

Grouping objects
IRanges internals

IRanges internals
IRanges-utils

IRanges utility functions
RangedData-class

Data on ranges
nearest-methods

Finding the nearest range neighbor
RangesList-class

List of Ranges
rdapply

Applying over spaces
DataFrameList-class

List of DataFrames
Rle-class-leftovers

Rle objects (old man page)
expand

The expand method for uncompressing compressed data columns
Views-class

Views objects
view-summarization-methods

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

The RleViews class
inter-range-methods

Inter range transformations of a Ranges, Views, RangesList, MaskCollection, or RangedData object
CompressedList-class

CompressedList objects
IntervalForest-class

Interval Search Forests
AtomicList

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

Lists of RangedData
RangedSelection-class

Selection of ranges and columns
Ranges-class

Ranges objects
ViewsList-class

List of Views
Ranges-comparison

Comparing and ordering ranges