IRanges v2.6.1

Infrastructure for manipulating intervals on sequences

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.

Functions in IRanges

Name Description
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
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Encoding UTF-8
biocViews Infrastructure, DataRepresentation
LinkingTo S4Vectors
License Artistic-2.0
Collate Vector-class-leftovers.R List-class-leftovers.R AtomicList-class.R Ranges-class.R Ranges-comparison.R IRanges-class.R IRanges-constructor.R IRanges-utils.R Views-class.R Grouping-class.R CompressedList-class.R CompressedList-comparison.R Rle-class-leftovers.R RleViews-class.R RleViews-utils.R extractList.R seqapply.R multisplit.R AtomicList-impl.R AtomicList-utils.R ListGrouping-class.R Hits-class-leftovers.R DataFrame-utils.R DataFrameList-class.R DataFrameList-utils.R RangesList-class.R GappedRanges-class.R ViewsList-class.R RleViewsList-class.R RleViewsList-utils.R MaskCollection-class.R RangedData-class.R RDApplyParams-class.R RangedData-utils.R CompressedHitsList-class.R NCList-class.R RangedSelection-class.R read.Mask.R findOverlaps-methods.R intra-range-methods.R inter-range-methods.R reverse-methods.R coverage-methods.R slice-methods.R setops-methods.R nearest-methods.R cbind-Rle-methods.R tile-methods.R subsetting-internals.R zzz.R

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