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IRanges (version 2.2.9)

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

2.2.9

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in IRanges (2.2.9)

FilterRules-class

Collection of Filter Rules
RangedData-class

Data on ranges
nearest-methods

Finding the nearest range neighbor
IRanges-constructor

The IRanges constructor and supporting functions
findOverlaps-methods

Finding overlapping ranges
IRanges-class

IRanges and NormalIRanges objects
Ranges-class

Ranges objects
Ranges-comparison

Comparing and ordering ranges
extractList

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

Matrix for Filter Results
inter-range-methods

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

List of Views
IntervalForest-class

Interval Search Forests
DataFrameList-class

List of DataFrames
expand

The expand method for uncompressing compressed data columns
GappedRanges-class

GappedRanges objects
Grouping-class

Grouping objects
MaskCollection-class

MaskCollection objects
mapCoords-methods

Mapping of ranges to another sequence
RleViews-class

The RleViews class
Rle-class-leftovers

Rle objects (old man page)
setops-methods

Set operations on IRanges and RangesList objects
seqapply

Apply function and cast to Vector
RleViewsList-class

List of RleViews
slice-methods

Slice a vector-like or list-like object
coverage-methods

Coverage of a set of ranges
DataFrame-utils

Common operations on DataFrame objects
IRanges internals

IRanges internals
IRanges-utils

IRanges utility functions
RangesList-class

List of Ranges
rdapply

Applying over spaces
Hits-class-leftovers

Examples of basic manipulation of Hits objects
HitsList-class

List of Hits objects
multisplit

Split elements belonging to multiple groups
NCList-class

Nested Containment List objects
read.Mask

Read a mask from a file
reverse

reverse
updateObject-methods

Update an object of a class defined in the IRanges package to its current class definition
Vector-class-leftovers

Vector objects (old man page)
AtomicList

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

CompressedList objects
IntervalTree-class

Interval Search Trees
intra-range-methods

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

List objects (old man page)
IRangesList-class

List of IRanges and NormalIRanges
RangedSelection-class

Selection of ranges and columns
RangedDataList-class

Lists of RangedData
view-summarization-methods

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

Views objects