S4Vectors: S4 implementation of vectors and lists

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Author
H. Pag├Ęs, M. Lawrence and P. Aboyoun
Date of publication
None
Maintainer
Bioconductor Package Maintainer <maintainer@bioconductor.org>
License
Artistic-2.0
Version
0.12.1

View on Bioconductor

Man pages

aggregate-methods
Compute summary statistics of subsets of vector-like objects
Annotated-class
Annotated class
DataFrame-class
DataFrame objects
DataTable-class
DataTable objects
expand-methods
Unlist the list-like columns of a DataFrame object
FilterMatrix-class
Matrix for Filter Results
FilterRules-class
Collection of Filter Rules
Hits-class
Hits objects
Hits-comparison
Comparing and ordering hits
HitsList-class
List of Hits objects
Hits-setops
Set operations on Hits objects
isSorted
Test if a vector-like object is sorted
List-class
List objects
List-utils
Common operations on List objects
Pairs-class
Pairs objects
Rle-class
Rle objects
Rle-runstat
Fixed-width running window summaries
Rle-utils
Common operations on Rle objects
S4Vectors-internals
S4Vectors internals
shiftApply-methods
Apply a function over subsequences of 2 vector-like objects
SimpleList-class
SimpleList objects
split-methods
Divide a vector-like object into groups
str-utils
Some utility functions to operate on strings
subsetting-utils
Subsetting utilities
Vector-class
Vector objects
Vector-comparison
Compare, order, tabulate vector-like objects
Vector-merge
Merge vector-like objects
Vector-setops
Set operations on vector-like objects
zip-methods
Convert between parallel vectors and lists

Files in this package

S4Vectors/DESCRIPTION
S4Vectors/NAMESPACE
S4Vectors/NEWS
S4Vectors/R
S4Vectors/R/Annotated-class.R
S4Vectors/R/DataFrame-class.R
S4Vectors/R/DataTable-class.R
S4Vectors/R/FilterRules-class.R
S4Vectors/R/Hits-class.R
S4Vectors/R/Hits-comparison.R
S4Vectors/R/Hits-setops.R
S4Vectors/R/HitsList-class.R
S4Vectors/R/List-class.R
S4Vectors/R/List-comparison.R
S4Vectors/R/List-utils.R
S4Vectors/R/Pairs-class.R
S4Vectors/R/Rle-class.R
S4Vectors/R/Rle-utils.R
S4Vectors/R/S4-utils.R
S4Vectors/R/SimpleList-class.R
S4Vectors/R/Vector-class.R
S4Vectors/R/Vector-comparison.R
S4Vectors/R/Vector-merge.R
S4Vectors/R/Vector-setops.R
S4Vectors/R/aggregate-methods.R
S4Vectors/R/eval-utils.R
S4Vectors/R/expand-methods.R
S4Vectors/R/int-utils.R
S4Vectors/R/isSorted.R
S4Vectors/R/logical-utils.R
S4Vectors/R/normarg-utils.R
S4Vectors/R/shiftApply-methods.R
S4Vectors/R/show-utils.R
S4Vectors/R/split-methods.R
S4Vectors/R/str-utils.R
S4Vectors/R/subsetting-utils.R
S4Vectors/R/utils.R
S4Vectors/R/vector-utils.R
S4Vectors/R/zzz.R
S4Vectors/TODO
S4Vectors/build
S4Vectors/build/vignette.rds
S4Vectors/inst
S4Vectors/inst/doc
S4Vectors/inst/doc/HTS_core_package_stack.txt
S4Vectors/inst/doc/RleTricks.R
S4Vectors/inst/doc/RleTricks.Rnw
S4Vectors/inst/doc/RleTricks.pdf
S4Vectors/inst/doc/S4QuickOverview.R
S4Vectors/inst/doc/S4QuickOverview.Rnw
S4Vectors/inst/doc/S4QuickOverview.pdf
S4Vectors/inst/include
S4Vectors/inst/include/S4Vectors_defines.h
S4Vectors/inst/include/S4Vectors_interface.h
S4Vectors/inst/include/_S4Vectors_stubs.c
S4Vectors/inst/unitTests
S4Vectors/inst/unitTests/test_DataFrame-class.R
S4Vectors/inst/unitTests/test_DataTable-class.R
S4Vectors/inst/unitTests/test_FilterRules.R
S4Vectors/inst/unitTests/test_Hits-class.R
S4Vectors/inst/unitTests/test_List-class.R
S4Vectors/inst/unitTests/test_List-utils.R
S4Vectors/inst/unitTests/test_Pairs-class.R
S4Vectors/inst/unitTests/test_Rle-class.R
S4Vectors/inst/unitTests/test_Rle-utils.R
S4Vectors/inst/unitTests/test_Vector-merge.R
S4Vectors/inst/unitTests/test_expand-methods.R
S4Vectors/man
S4Vectors/man/Annotated-class.Rd
S4Vectors/man/DataFrame-class.Rd
S4Vectors/man/DataTable-class.Rd
S4Vectors/man/FilterMatrix-class.Rd
S4Vectors/man/FilterRules-class.Rd
S4Vectors/man/Hits-class.Rd
S4Vectors/man/Hits-comparison.Rd
S4Vectors/man/Hits-setops.Rd
S4Vectors/man/HitsList-class.Rd
S4Vectors/man/List-class.Rd
S4Vectors/man/List-utils.Rd
S4Vectors/man/Pairs-class.Rd
S4Vectors/man/Rle-class.Rd
S4Vectors/man/Rle-runstat.Rd
S4Vectors/man/Rle-utils.Rd
S4Vectors/man/S4Vectors-internals.Rd
S4Vectors/man/SimpleList-class.Rd
S4Vectors/man/Vector-class.Rd
S4Vectors/man/Vector-comparison.Rd
S4Vectors/man/Vector-merge.Rd
S4Vectors/man/Vector-setops.Rd
S4Vectors/man/aggregate-methods.Rd
S4Vectors/man/expand-methods.Rd
S4Vectors/man/isSorted.Rd
S4Vectors/man/shiftApply-methods.Rd
S4Vectors/man/split-methods.Rd
S4Vectors/man/str-utils.Rd
S4Vectors/man/subsetting-utils.Rd
S4Vectors/man/zip-methods.Rd
S4Vectors/src
S4Vectors/src/AEbufs.c
S4Vectors/src/DataFrame_class.c
S4Vectors/src/Hits_class.c
S4Vectors/src/List_class.c
S4Vectors/src/R_init_S4Vectors.c
S4Vectors/src/Rle_class.c
S4Vectors/src/Rle_utils.c
S4Vectors/src/S4Vectors.h
S4Vectors/src/SEXP_utils.c
S4Vectors/src/SimpleList_class.c
S4Vectors/src/anyMissing.c
S4Vectors/src/eval_utils.c
S4Vectors/src/hash_utils.c
S4Vectors/src/int_utils.c
S4Vectors/src/logical_utils.c
S4Vectors/src/safe_arithm.c
S4Vectors/src/sort_utils.c
S4Vectors/src/str_utils.c
S4Vectors/src/vector_utils.c
S4Vectors/tests
S4Vectors/tests/run_unitTests.R
S4Vectors/vignettes
S4Vectors/vignettes/RleTricks.Rnw
S4Vectors/vignettes/S4QuickOverview.Rnw
S4Vectors/vignettes/slides.sty