Learn R Programming

⚠️There's a newer version (2.6.1) of this package.Take me there.

IRanges (version 2.0.1)

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.

Copy Link

Version

Version

2.0.1

License

Artistic-2.0

Maintainer

Bioconductor Package Maintainer

Last Published

February 15th, 2017

Functions in IRanges (2.0.1)

coverage-methods

Coverage of a set of ranges
DataFrame-utils

Common operations on DataFrame objects
IntervalForest-class

Interval Search Forests
inter-range-methods

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

List of IRanges and NormalIRanges
List-class-leftovers

List objects (old man page)
RangesList-class

List of Ranges
rdapply

Applying over spaces
slice-methods

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

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

List of DataFrames
expand

The expand method for uncompressing compressed data columns
Grouping-class

Grouping objects
GappedRanges-class

GappedRanges objects
map-methods

Mapping of ranges to another sequence
extractList

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

Matrix for Filter Results
IRanges-class

IRanges and NormalIRanges objects
IRanges-constructor

The IRanges constructor and supporting functions
nearest-methods

Finding the nearest range neighbor
RangedData-class

Data on ranges
Rle-class-leftovers

Rle objects (old man page)
RleViews-class

The RleViews class
RleViewsList-class

List of RleViews
score

Score accessor and setter
mapCoords-methods

Mapping of ranges to another sequence
read.Mask

Read a mask from a file
reverse

reverse
seqapply

Apply function and cast to Vector
setops-methods

Set operations on IRanges, RangesList, and Hits objects
FilterRules-class

Collection of Filter Rules
findOverlaps-methods

Finding overlapping ranges
Hits-class-leftovers

Examples of basic manipulation of Hits objects
RangedDataList-class

Lists of RangedData
HitsList-class

List of Hits objects
RangedSelection-class

Selection of ranges and columns
IntervalTree-class

Interval Search Trees
intra-range-methods

Intra range transformations of a Ranges, Views, RangesList, or MaskCollection object
IRanges internals

IRanges internals
IRanges-utils

IRanges utility functions
Vector-class-leftovers

Vector objects (old man page)
view-summarization-methods

Summarize views on a vector-like object with numeric values
AtomicList

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

CompressedList objects
MaskCollection-class

MaskCollection objects
multisplit

Split elements belonging to multiple groups
Ranges-class

Ranges objects
Ranges-comparison

Comparing and ordering ranges
Views-class

Views objects
ViewsList-class

List of Views