XVector: Representation and manpulation of external sequences
Version 0.16.0

Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).

AuthorHervé Pagès and Patrick Aboyoun
Bioconductor views DataRepresentation Infrastructure
Date of publicationNone
MaintainerHervé Pagès <hpages@fredhutch.org>
LicenseArtistic-2.0
Version0.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("XVector")

Popular man pages

compact-methods: Object compaction
intra-range-methods: Intra range transformations of an XVectorList object
reverse-methods: Reverse an XVector or XVectorList object
view-summarization-methods: Summarize views on an XInteger or XDouble object
XIntegerViews-class: The XIntegerViews class
XRawList-class: XRawList objects
XVector-class: XVector objects
See all...

All man pages Function index File listing

Man pages

compact-methods: Object compaction
intra-range-methods: Intra range transformations of an XVectorList object
OnDiskRaw-class: OnDiskRaw objects
reverse-methods: Reverse an XVector or XVectorList object
slice-methods: Slice an XInteger or XDouble object
updateObject-methods: Update an object of a class defined in the XVector package to...
view-summarization-methods: Summarize views on an XInteger or XDouble object
XDoubleViews-class: The XDoubleViews class
XIntegerViews-class: The XIntegerViews class
XRawList-class: XRawList objects
XRawList-comparison: Comparing and ordering the list elements of XRawList objects
XVector-class: XVector objects
XVector-internals: XVector internals
XVectorList-class: XVectorList objects

Functions

!=,SharedVector,SharedVector-method Man page
<=,XRawList,XRawList-method Man page
==,SharedVector,SharedVector-method Man page
==,XDouble,XDoubleViews-method Man page
==,XDoubleViews,XDouble-method Man page
==,XDoubleViews,XDoubleViews-method Man page
==,XDoubleViews,numeric-method Man page
==,XInteger,XIntegerViews-method Man page
==,XIntegerViews,XInteger-method Man page
==,XIntegerViews,XIntegerViews-method Man page
==,XIntegerViews,integer-method Man page
==,XRawList,XRawList-method Man page
==,XVector,XVector-method Man page
==,integer,XIntegerViews-method Man page
==,numeric,XDoubleViews-method Man page
DirectRaw Source code
GroupedIRanges Man page
GroupedIRanges-class Man page
OnDiskRaw Man page
OnDiskRaw-class Man page
RdaCollection Source code
SerializedRaw Source code
SharedDouble Man page Source code
SharedDouble-class Man page
SharedDouble.read Source code
SharedDouble.write Source code
SharedInteger Man page Source code
SharedInteger-class Man page
SharedInteger.read Source code
SharedInteger.write Source code
SharedRaw Man page Source code
SharedRaw-class Man page
SharedRaw.read Man page Source code
SharedRaw.readComplexes Man page Source code
SharedRaw.readInts Man page Source code
SharedRaw.write Man page Source code
SharedRaw.writeInts Man page Source code
SharedRaw_Pool Man page
SharedRaw_Pool-class Man page
SharedVector Man page Source code
SharedVector-class Man page
SharedVector.compare Man page Source code
SharedVector.copy Man page Source code
SharedVector.mcopy Source code
SharedVector.reverseCopy Source code
SharedVector_Pool Man page
SharedVector_Pool-class Man page
Views,XDouble-method Man page
Views,XInteger-method Man page
Views,integer-method Man page
Views,numeric-method Man page
XDouble Man page Source code
XDouble-class Man page
XDoubleViews Man page
XDoubleViews-class Man page
XDoubleViews.equal Source code
XDoubleViews.show_vframe Source code
XDoubleViews.show_vframe_header Source code
XDoubleViews.show_vframe_line Source code
XDoubleViews.view1_equal_view2 Source code
XInteger Man page Source code
XInteger-class Man page
XIntegerViews Man page
XIntegerViews-class Man page
XIntegerViews.equal Source code
XIntegerViews.show_vframe Source code
XIntegerViews.show_vframe_header Source code
XIntegerViews.show_vframe_line Source code
XIntegerViews.view1_equal_view2 Source code
XNumeric Man page Source code
XRaw Man page Source code
XRaw-class Man page
XRawList Man page
XRawList-class Man page
XRawList-comparison Man page
XVector Man page
XVector-class Man page
XVector.equal Source code
XVectorList Man page Source code
XVectorList-class Man page
XVectorList.getElement Source code
[,SharedVector_Pool-method Man page
[,XVector-method Man page
[,XVectorList-method Man page
[[,SharedRaw_Pool-method Man page
[[,XVectorList-method Man page
[[<-,SharedRaw_Pool-method Man page
[[<-,XVectorList-method Man page
address Source code
address0 Source code
addresses Source code
as.data.frame,GroupedIRanges-method Man page
as.integer,SharedInteger-method Man page
as.integer,SharedRaw-method Man page
as.integer,XInteger-method Man page
as.integer,XRaw-method Man page
as.numeric,SharedDouble-method Man page
as.numeric,SharedVector-method Man page
as.numeric,XDouble-method Man page
as.numeric,XVector-method Man page
as.raw,XRaw-method Man page
as.vector,XDouble-method Man page
as.vector,XInteger-method Man page
as.vector,XRaw-method Man page
c,GroupedIRanges-method Man page
c,SharedVector_Pool-method Man page
c,XVector-method Man page
c,XVectorList-method Man page
check_objname Source code
class:GroupedIRanges Man page
class:OnDiskRaw Man page
class:SharedDouble Man page
class:SharedInteger Man page
class:SharedRaw Man page
class:SharedRaw_Pool Man page
class:SharedVector Man page
class:SharedVector_Pool Man page
class:XDouble Man page
class:XDoubleViews Man page
class:XInteger Man page
class:XIntegerViews Man page
class:XRaw Man page
class:XRawList Man page
class:XVector Man page
class:XVectorList Man page
coerce,SharedVector,SharedVector_Pool-method Man page
coerce,integer,XVector-method Man page
coerce,numeric,XDouble-method Man page
coerce,numeric,XInteger-method Man page
coerce,numeric,XRaw-method Man page
coerce,numeric,XVector-method Man page
coerce,raw,XRaw-method Man page
coerce,raw,XVector-method Man page
compact Man page
compact,ANY-method Man page
compact,XVector-method Man page
compact,XVectorList-method Man page
dec_NLINKS Source code
dropDuplicatedPoolElts Source code
dropUnusedPoolElts Source code
duplicated,XRawList-method Man page
duplicated.XRawList Man page Source code Source code
elementNROWS,XVectorList-method Man page
endoapply,XVectorList-method Man page
finalize_filexp Source code
getFileSize Source code
getFirstObjectInfoFromRda Source code
getRdaTypeAndFormat Source code
get_filepos Source code
get_rdapath Source code
get_tag Source code
intra-range-methods Man page
is.unsorted,XRawList-method Man page
length,OnDiskRaw-method Man page
length,SharedVector-method Man page
length,SharedVector_Pool-method Man page
length,XVector-method Man page
length,XVectorList-method Man page
loadSequence Source code
loadSequenceFromRda Source code
load_serialized_object Source code
makeLinkToCachedObject Source code
match,XRawList,XRawList-method Man page
names,XVectorList-method Man page
names<-,XVectorList-method Man page
narrow Man page
narrow,XVectorList-method Man page
nc_NLINKS Source code
newExternalptrWithTag Source code
new_SharedVector_Pool_from_SharedVector Source code
new_SharedVector_Pool_from_list_of_SharedVector Source code
new_XVectorList_from_list_of_XVector Source code
new_input_filexp Source code
new_output_filexp Source code
normargLength Source code
normargOffset Source code
normarg_compress Source code
normarg_compression_level Source code
normarg_input_filepath Source code
onLoad Source code
onUnload Source code
oneLineDesc Source code
open_input_files Source code
open_output_file Source code
order,XRawList-method Man page
pcompare Man page
pcompare,XRawList,XRawList-method Man page
problemIfNotExternalVector Source code
rank,XRawList-method Man page
readBin2 Source code
readXRaw Source code
rev,XVector-method Man page
reverse,SharedRaw-method Man page
reverse,SharedVector_Pool-method Man page
reverse,XVector-method Man page
reverse,XVectorList-method Man page
reverse-methods Man page
rewind_filexp Source code
selfmatchXRawList Source code
set_filepos Source code
set_tag Source code
show,GroupedIRanges-method Man page
show,SharedVector-method Man page
show,SharedVector_Pool-method Man page
show,XDouble-method Man page
show,XDoubleViews-method Man page
show,XIntegerViews-method Man page
show,XVector-method Man page
show,externalptr-method Man page
showAsCell,XVectorList-method Man page
sizeOnDisk Source code
skipBytes Source code
slice,XDouble-method Man page
slice,XInteger-method Man page
slice,integer-method Man page
slice,numeric-method Man page
slice-methods Man page
subseq Man page
subseq,XVector-method Man page
subseq,XVectorList-method Man page
subseq<- Man page
subseq<-,XVector-method Man page
tagIsVector Source code
taglength Source code
tagtype Source code
test Source code
threebands Man page
threebands,XVectorList-method Man page
toString,SharedRaw-method Man page
unlist_list_of_XVectorList Man page Source code
unsafe.extractList Source code
unsplit_list_of_XVectorList Man page Source code
updateObject,XIntegerViews-method Man page
updateObject,XVector-method Man page
updateObject-methods Man page
valid.GroupedIRanges Source code
valid.RdaCollection Source code
valid.SharedDouble Source code
valid.SharedInteger Source code
valid.SharedRaw Source code
valid.SharedRaw_Pool Source code
valid.SharedVector Source code
valid.SharedVector_Pool Source code
view-summarization-methods Man page
viewMaxs,XDoubleViews-method Man page
viewMaxs,XIntegerViews-method Man page
viewMeans,XDoubleViews-method Man page
viewMeans,XIntegerViews-method Man page
viewMins,XDoubleViews-method Man page
viewMins,XIntegerViews-method Man page
viewSums,XDoubleViews-method Man page
viewSums,XIntegerViews-method Man page
viewWhichMaxs,XDoubleViews-method Man page
viewWhichMaxs,XIntegerViews-method Man page
viewWhichMins,XDoubleViews-method Man page
viewWhichMins,XIntegerViews-method Man page
width,SharedVector_Pool-method Man page
width,XVectorList-method Man page
xvcopy Man page
xvcopy,SharedVector-method Man page
xvcopy,SharedVector_Pool-method Man page
xvcopy,XRawList-method Man page
xvcopy,XVector-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/OnDiskRaw-class.R
R/RdaCollection-class.R
R/SharedDouble-class.R
R/SharedInteger-class.R
R/SharedRaw-class.R
R/SharedVector-class.R
R/XDouble-class.R
R/XDoubleViews-class.R
R/XInteger-class.R
R/XIntegerViews-class.R
R/XRaw-class.R
R/XRawList-class.R
R/XRawList-comparison.R
R/XVector-class.R
R/XVectorList-class.R
R/compact-methods.R
R/intra-range-methods.R
R/io-utils.R
R/reverse-methods.R
R/slice-methods.R
R/updateObject-methods.R
R/view-summarization-methods.R
R/zzz.R
TODO
inst
inst/include
inst/include/XVector_defines.h
inst/include/XVector_interface.h
inst/include/_XVector_stubs.c
inst/unitTests
inst/unitTests/test_slice-methods.R
inst/unitTests/test_view-summarization-methods.R
man
man/OnDiskRaw-class.Rd
man/XDoubleViews-class.Rd
man/XIntegerViews-class.Rd
man/XRawList-class.Rd
man/XRawList-comparison.Rd
man/XVector-class.Rd
man/XVector-internals.Rd
man/XVectorList-class.Rd
man/compact-methods.Rd
man/intra-range-methods.Rd
man/reverse-methods.Rd
man/slice-methods.Rd
man/updateObject-methods.Rd
man/view-summarization-methods.Rd
src
src/IRanges_stubs.c
src/Makevars
src/Makevars.win
src/Ocopy_byteblocks.c
src/R_init_XVector.c
src/S4Vectors_stubs.c
src/SharedDouble_class.c
src/SharedInteger_class.c
src/SharedRaw_class.c
src/SharedVector_class.c
src/XRawList_comparison.c
src/XVector.h
src/XVectorList_class.c
src/XVector_class.c
src/io_utils.c
src/slice_methods.c
src/vector_copy.c
src/view_summarization_methods.c
tests
tests/run_unitTests.R
XVector documentation built on May 20, 2017, 10:34 p.m.

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