IRanges: Infrastructure for manipulating intervals on sequences

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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.

Author
H. Pag├Ęs, P. Aboyoun and M. Lawrence
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
2.8.1

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