IRanges: Infrastructure for manipulating intervals on sequences

Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.

AuthorH. Pag├Ęs, P. Aboyoun and M. Lawrence
Date of publicationNone
MaintainerBioconductor Package Maintainer <maintainer@bioconductor.org>
LicenseArtistic-2.0
Version2.8.1

View on Bioconductor

Man pages

AtomicList-class: Lists of Atomic Vectors in Natural and Rle Form

AtomicList-utils: Common operations on AtomicList objects

bind-arrays: Bind arrays along their rows or columns

CompressedHitsList-class: CompressedHitsList objects

CompressedList-class: CompressedList objects

coverage-methods: Coverage of a set of ranges

DataFrameList-class: List of DataFrames

DataFrame-utils: Common operations on DataFrame objects

extractList: Group elements of a vector-like object into a list-like...

findOverlaps-methods: Finding overlapping ranges

GappedRanges-class: GappedRanges objects (DEFUNCT!)

Grouping-class: Grouping objects

Hits-class-leftovers: Examples of basic manipulation of Hits objects

inter-range-methods: Inter range transformations of a Ranges, Views, RangesList,...

intra-range-methods: Intra range transformations of a Ranges, Views, RangesList,...

IRanges-class: IRanges and NormalIRanges objects

IRanges-constructor: The IRanges constructor and supporting functions

IRanges-internals: IRanges internals

IRangesList-class: List of IRanges and NormalIRanges

IRanges-utils: IRanges utility functions

List-class-leftovers: List objects (old man page)

MaskCollection-class: MaskCollection objects

multisplit: Split elements belonging to multiple groups

NCList-class: Nested Containment List objects

nearest-methods: Finding the nearest range neighbor

RangedData-class: Data on ranges

RangedDataList-class: Lists of RangedData (DEFUNCT!)

RangedSelection-class: Selection of ranges and columns

Ranges-class: Ranges objects

Ranges-comparison: Comparing and ordering ranges

RangesList-class: List of Ranges

RDApplyParams-class: Applying over spaces (DEFUNCT!)

read.Mask: Read a mask from a file

reverse-methods: reverse

Rle-class-leftovers: Rle objects (old man page)

RleViews-class: The RleViews class

RleViewsList-class: List of RleViews

seqapply: 2 methods that should be documented somewhere else

setops-methods: Set operations on Ranges and RangesList objects

slice-methods: Slice a vector-like or list-like object

Vector-class-leftovers: Vector objects (old man page)

Views-class: Views objects

ViewsList-class: List of Views

view-summarization-methods: Summarize views on a vector-like object with numeric values

Files in this package

IRanges/DESCRIPTION
IRanges/NAMESPACE
IRanges/NEWS
IRanges/R
IRanges/R/AtomicList-class.R IRanges/R/AtomicList-impl.R IRanges/R/AtomicList-utils.R IRanges/R/CompressedHitsList-class.R IRanges/R/CompressedList-class.R IRanges/R/CompressedList-comparison.R IRanges/R/DataFrame-utils.R IRanges/R/DataFrameList-class.R IRanges/R/DataFrameList-utils.R IRanges/R/GappedRanges-class.R IRanges/R/Grouping-class.R IRanges/R/Hits-class-leftovers.R IRanges/R/IRanges-class.R IRanges/R/IRanges-constructor.R IRanges/R/IRanges-utils.R IRanges/R/List-class-leftovers.R IRanges/R/ListGrouping-class.R IRanges/R/MaskCollection-class.R IRanges/R/NCList-class.R IRanges/R/RDApplyParams-class.R IRanges/R/RangedData-class.R IRanges/R/RangedData-utils.R IRanges/R/RangedSelection-class.R IRanges/R/Ranges-class.R IRanges/R/Ranges-comparison.R IRanges/R/RangesList-class.R IRanges/R/Rle-class-leftovers.R IRanges/R/RleViews-class.R IRanges/R/RleViews-utils.R IRanges/R/RleViewsList-class.R IRanges/R/RleViewsList-utils.R IRanges/R/Vector-class-leftovers.R IRanges/R/Views-class.R IRanges/R/ViewsList-class.R IRanges/R/bind-arrays.R IRanges/R/cbind-Rle-methods.R IRanges/R/coverage-methods.R IRanges/R/extractList.R IRanges/R/findOverlaps-methods.R IRanges/R/inter-range-methods.R IRanges/R/intra-range-methods.R IRanges/R/multisplit.R IRanges/R/nearest-methods.R IRanges/R/read.Mask.R IRanges/R/reverse-methods.R IRanges/R/seqapply.R IRanges/R/setops-methods.R IRanges/R/slice-methods.R IRanges/R/subsetting-utils.R IRanges/R/tile-methods.R IRanges/R/zzz.R
IRanges/TODO
IRanges/build
IRanges/build/vignette.rds
IRanges/inst
IRanges/inst/CITATION
IRanges/inst/doc
IRanges/inst/doc/IRangesOverview.R
IRanges/inst/doc/IRangesOverview.Rnw
IRanges/inst/doc/IRangesOverview.pdf
IRanges/inst/extdata
IRanges/inst/extdata/ce2chrM.bed
IRanges/inst/extdata/ce2chrM.fa.out
IRanges/inst/extdata/hg18liftAll.lft
IRanges/inst/extdata/hs_b36v3_chrY.agp
IRanges/inst/include
IRanges/inst/include/IRanges_defines.h
IRanges/inst/include/IRanges_interface.h
IRanges/inst/include/_IRanges_stubs.c
IRanges/inst/unitTests
IRanges/inst/unitTests/test_AtomicList-class.R
IRanges/inst/unitTests/test_AtomicList-utils.R
IRanges/inst/unitTests/test_DataFrame-utils.R
IRanges/inst/unitTests/test_DataFrameList.R
IRanges/inst/unitTests/test_Grouping-class.R
IRanges/inst/unitTests/test_HitsList.R
IRanges/inst/unitTests/test_IRanges-class.R
IRanges/inst/unitTests/test_NCList-class.R
IRanges/inst/unitTests/test_Ranges-comparison.R
IRanges/inst/unitTests/test_RangesList-class.R
IRanges/inst/unitTests/test_RleViews.R
IRanges/inst/unitTests/test_RleViewsList.R
IRanges/inst/unitTests/test_bind-arrays.R
IRanges/inst/unitTests/test_coverage-methods.R
IRanges/inst/unitTests/test_extractList.R
IRanges/inst/unitTests/test_findOverlaps-methods.R
IRanges/inst/unitTests/test_inter-range-methods.R
IRanges/inst/unitTests/test_intra-range-methods.R
IRanges/inst/unitTests/test_nearest-methods.R
IRanges/inst/unitTests/test_seqapply.R
IRanges/inst/unitTests/test_setops-methods.R
IRanges/inst/unitTests/test_tile-methods.R
IRanges/man
IRanges/man/AtomicList-class.Rd IRanges/man/AtomicList-utils.Rd IRanges/man/CompressedHitsList-class.Rd IRanges/man/CompressedList-class.Rd IRanges/man/DataFrame-utils.Rd IRanges/man/DataFrameList-class.Rd IRanges/man/GappedRanges-class.Rd IRanges/man/Grouping-class.Rd IRanges/man/Hits-class-leftovers.Rd IRanges/man/IRanges-class.Rd IRanges/man/IRanges-constructor.Rd IRanges/man/IRanges-internals.Rd IRanges/man/IRanges-utils.Rd IRanges/man/IRangesList-class.Rd IRanges/man/List-class-leftovers.Rd IRanges/man/MaskCollection-class.Rd IRanges/man/NCList-class.Rd IRanges/man/RDApplyParams-class.Rd IRanges/man/RangedData-class.Rd IRanges/man/RangedDataList-class.Rd IRanges/man/RangedSelection-class.Rd IRanges/man/Ranges-class.Rd IRanges/man/Ranges-comparison.Rd IRanges/man/RangesList-class.Rd IRanges/man/Rle-class-leftovers.Rd IRanges/man/RleViews-class.Rd IRanges/man/RleViewsList-class.Rd IRanges/man/Vector-class-leftovers.Rd IRanges/man/Views-class.Rd IRanges/man/ViewsList-class.Rd IRanges/man/bind-arrays.Rd IRanges/man/coverage-methods.Rd IRanges/man/extractList.Rd IRanges/man/findOverlaps-methods.Rd IRanges/man/inter-range-methods.Rd IRanges/man/intra-range-methods.Rd IRanges/man/multisplit.Rd IRanges/man/nearest-methods.Rd IRanges/man/read.Mask.Rd IRanges/man/reverse-methods.Rd IRanges/man/seqapply.Rd IRanges/man/setops-methods.Rd IRanges/man/slice-methods.Rd IRanges/man/view-summarization-methods.Rd
IRanges/src
IRanges/src/CompressedAtomicList_utils.c
IRanges/src/CompressedIRangesList_class.c
IRanges/src/CompressedList_class.c
IRanges/src/Grouping_class.c
IRanges/src/IRanges.h
IRanges/src/IRanges_class.c
IRanges/src/IRanges_constructor.c
IRanges/src/NCList.c
IRanges/src/R_init_IRanges.c
IRanges/src/Ranges_class.c
IRanges/src/Ranges_comparison.c
IRanges/src/RleViews_utils.c
IRanges/src/S4Vectors_stubs.c
IRanges/src/SimpleRangesList_class.c
IRanges/src/coverage_methods.c
IRanges/src/inter_range_methods.c
IRanges/tests
IRanges/tests/run_unitTests.R
IRanges/vignettes
IRanges/vignettes/IRangesOverview.Rnw

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