GenomicTuples: Representation and Manipulation of Genomic Tuples
Version 1.10.0

GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.

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AuthorPeter Hickey <peter.hickey@gmail.com>, with contributions from Marcin Cieslik and Herve Pages.
Bioconductor views DataRepresentation Infrastructure Sequencing
Date of publicationNone
MaintainerPeter Hickey <peter.hickey@gmail.com>
LicenseArtistic-2.0
Version1.10.0
URL www.github.com/PeteHaitch/GenomicTuples
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicTuples")

Man pages

findOverlaps-methods: Finding overlapping genomic tuples
GenomicTuples-package: Representation and manipulation of genomic tuples.
GTuples-class: GTuples objects
GTuples-comparison: Comparing and ordering genomic tuples
GTuplesList-class: GTuplesList objects
illdefined-methods: Undefined methods
intra-tuple-methods: Intra-tuple transformations of a GTuples or GTuplesLists...
nearest-methods: Finding the nearest genomic tuple/range neighbour
tuples-squeezers: Squeeze the tuples out of a tuples-based object

Functions

$,GTuples-method Man page
$<-,GTuples,numeric-method Man page
GT2DT Source code
GTuples Man page Man page Source code
GTuples-class Man page
GTuples-comparison Man page
GTuples.asIntegerTuples Source code
GTuplesList Man page Man page Source code
GTuplesList-class Man page
GenomicTuples-package Man page
IPD Man page
IPD,GTuples-method Man page
IPD,GTuplesList-method Man page
IPDCpp Source code
Ops,GTuples,numeric-method Man page
[,GTuples-method Man page
[,GTuplesList,ANY-method Man page
[<-,GTuples-method Man page
[<-,GTuplesList,ANY,ANY,ANY-method Man page
[[<-,GTuplesList,ANY,ANY,ANY-method Man page
allTuplesSortedCpp Source code
as.character,GTuples-method Man page
as.data.frame,GTuples-method Man page
as.factor,GTuples-method Man page
c,GTuples-method Man page
class:GTuples Man page
class:GTuplesList Man page
coerce,GRanges,GTuples-method Man page
coerce,GTuplesList,GRangesList-method Man page
coerce,GTuplesList,data.frame-method Man page
coerce,GTuplesList,list-method Man page
countOverlaps Man page
countOverlaps,GTuples,GTuples-method Man page
countOverlaps,GTuples,GTuplesList-method Man page
countOverlaps,GTuples,GenomicRanges-method Man page
countOverlaps,GTuples,GenomicRangesList-method Man page
countOverlaps,GTuples,Vector-method Man page
countOverlaps,GTuplesList,GTuples-method Man page
countOverlaps,GTuplesList,GTuplesList-method Man page
countOverlaps,GTuplesList,GenomicRanges-method Man page
countOverlaps,GTuplesList,GenomicRangesList-method Man page
countOverlaps,GTuplesList,Vector-method Man page
countOverlaps,GenomicRanges,GTuples-method Man page
countOverlaps,GenomicRanges,GTuplesList-method Man page
countOverlaps,GenomicRangesList,GTuples-method Man page
countOverlaps,GenomicRangesList,GTuplesList-method Man page
countOverlaps,Vector,GTuples-method Man page
countOverlaps,Vector,GTuplesList-method Man page
countOverlaps.definition Source code
coverage,GTuples-method Man page
coverage,GTuplesList-method Man page
disjoin,GTuples-method Man page
disjoin,GTuplesList-method Man page
disjointBins,GTuples-method Man page
distance,GTuples,GTuples-method Man page
distanceToNearest,GTuples,GTuples-method Man page
distanceToNearest,GTuples,missing-method Man page
duplicated,GTuples-method Man page
duplicated.GTuples Man page Source code Source code
elementMetadata,GTuplesList-method Man page
elementMetadata<-,GTuples-method Man page
elementMetadata<-,GTuplesList-method Man page
end,GTuples-method Man page
end,GTuplesList-method Man page
end<-,GTuples-method Man page
end<-,GTuplesList-method Man page
findEqual.GTuples Source code
findOverlaps Man page
findOverlaps,GRangesList,GTuples-method Man page
findOverlaps,GRangesList,GTuplesList-method Man page
findOverlaps,GTuples,GRangesList-method Man page
findOverlaps,GTuples,GTuples-method Man page
findOverlaps,GTuples,GTuplesList-method Man page
findOverlaps,GTuples,GenomicRanges-method Man page
findOverlaps,GTuples,RangedData-method Man page
findOverlaps,GTuples,RangesList-method Man page
findOverlaps,GTuplesList,GRangesList-method Man page
findOverlaps,GTuplesList,GTuples-method Man page
findOverlaps,GTuplesList,GTuplesList-method Man page
findOverlaps,GTuplesList,GenomicRanges-method Man page
findOverlaps,GTuplesList,RangedData-method Man page
findOverlaps,GTuplesList,RangesList-method Man page
findOverlaps,GenomicRanges,GTuples-method Man page
findOverlaps,GenomicRanges,GTuplesList-method Man page
findOverlaps,RangedData,GTuples-method Man page
findOverlaps,RangedData,GTuplesList-method Man page
findOverlaps,RangesList,GTuples-method Man page
findOverlaps,RangesList,GTuplesList-method Man page
findOverlaps-methods Man page
flank,GTuples-method Man page
flank,GTuplesList-method Man page
follow,GTuples,GTuples-method Man page
follow,GTuples,missing-method Man page
gaps,GTuples-method Man page
granges,GTuples-method Man page
gtlist Man page
gtuples Man page
intersect,GTuples,GTuples-method Man page
intra-tuple-methods Man page
is.unsorted,GTuples-method Man page
isDisjoint,GTuples-method Man page
isDisjoint,GTuplesList-method Man page
length,GTuples-method Man page
makeNakedMatFromGTuples Source code
match,GTuples,GTuples-method Man page
matrixDiffWithRecycling Source code
names,GTuples-method Man page
names<-,GTuples-method Man page
narrow Man page
narrow,GTuples-method Man page
nearest,GTuples,GTuples-method Man page
nearest,GTuples,missing-method Man page
nearest-methods Man page
onUnload Source code
order,GTuples-method Man page
order.GTuples Source code
overlapsAny Man page
overlapsAny,GRanges,GTuples-method Man page
overlapsAny,GRanges,GTuplesList-method Man page
overlapsAny,GRangesList,GTuples-method Man page
overlapsAny,GRangesList,GTuplesList-method Man page
overlapsAny,GTuples,GRanges-method Man page
overlapsAny,GTuples,GRangesList-method Man page
overlapsAny,GTuples,GTuples-method Man page
overlapsAny,GTuples,GTuplesList-method Man page
overlapsAny,GTuples,RangedData-method Man page
overlapsAny,GTuples,RangesList-method Man page
overlapsAny,GTuplesList,GRanges-method Man page
overlapsAny,GTuplesList,GRangesList-method Man page
overlapsAny,GTuplesList,GTuples-method Man page
overlapsAny,GTuplesList,GtuplesList-method Man page
overlapsAny,GTuplesList,RangedData-method Man page
overlapsAny,GTuplesList,RangesList-method Man page
overlapsAny,RangedData,GTuples-method Man page
overlapsAny,RangedData,GTuplesList-method Man page
overlapsAny,RangesList,GTuples-method Man page
overlapsAny,RangesList,GTuplesList-method Man page
pcompare,GTuples,GTuples-method Man page
pcompareGTuplesCpp Source code
pcompare_GTuples Source code
pgap,GTuples,GTuples-method Man page
pintersect,GTuples,GTuples-method Man page
pintersect,GTuples,GTuplesList-method Man page
pintersect,GTuplesList,GTuples-method Man page
pintersect,GTuplesList,GTuplesList-method Man page
precede,GTuples,GTuples-method Man page
precede,GTuples,missing-method Man page
promoters,GTuples-method Man page
promoters,GTuplesList-method Man page
psetdiff,GTuples,GTuples-method Man page
psetdiff,GTuples,GTuplesList-method Man page
psetdiff,GTuplesList,GTuplesList-method Man page
punion,GTuples,GTuples-method Man page
punion,GTuples,GTuplesList-method Man page
punion,GTuplesList,GTuples-method Man page
range,GTuples-method Man page
range,GTuplesList-method Man page
ranges,GTuples-method Man page
ranges,GTuplesList-method Man page
ranges<-,GTuples-method Man page
ranges<-,GTuplesList-method Man page
rank,GTuples-method Man page
reduce,GTuples-method Man page
reduce,GTuplesList-method Man page
relistToClass,GTuples-method Man page
replaceROWS,NULL-method Man page
resize,GTuples-method Man page
resize,GTuplesList-method Man page
restrict,GTuplesList-method Man page
score,GTuples-method Man page
score,GTuplesList-method Man page
score<-,GTuples-method Man page
score<-,GTuplesList-method Man page
selfmatch,GTuples-method Man page
seqinfo,GTuples-method Man page
seqinfo,GTuplesList-method Man page
seqinfo<-,GTuples-method Man page
seqinfo<-,GTuplesList-method Man page
seqnames,GTuples-method Man page
seqnames,GTuplesList-method Man page
seqnames<-,GTuples-method Man page
seqnames<-,GTuplesList-method Man page
setdiff,GTuples,GTuples-method Man page
shift Man page
shift,GTuples-method Man page
shift,GTuplesList-method Man page
show,GTuples-method Man page
show,GTuplesList-method Man page
showGTuples Source code
size Man page
size,GTuples-method Man page
size,GTuplesList-method Man page
sort,GTuples-method Man page
sort.GTuples Man page Source code Source code
start,GTuples-method Man page
start,GTuplesList-method Man page
start<-,GTuples-method Man page
start<-,GTuplesList-method Man page
strand,GTuples-method Man page
strand,GTuplesList-method Man page
strand<-,GTuples-method Man page
strand<-,GTuplesList,ANY-method Man page
strand<-,GTuplesList,character-method Man page
subsetByOverlaps Man page
subsetByOverlaps,GRanges,GTuples-method Man page
subsetByOverlaps,GRanges,GTuplesList-method Man page
subsetByOverlaps,GRangesList,GTuples-method Man page
subsetByOverlaps,GRangesList,GTuplesList-method Man page
subsetByOverlaps,GTuples,GRanges-method Man page
subsetByOverlaps,GTuples,GRangesList-method Man page
subsetByOverlaps,GTuples,GTuples-method Man page
subsetByOverlaps,GTuples,GTuplesList-method Man page
subsetByOverlaps,GTuples,RangedData-method Man page
subsetByOverlaps,GTuples,RangesList-method Man page
subsetByOverlaps,GTuplesList,GRanges-method Man page
subsetByOverlaps,GTuplesList,GRangesList-method Man page
subsetByOverlaps,GTuplesList,GTuples-method Man page
subsetByOverlaps,GTuplesList,GTuplesList-method Man page
subsetByOverlaps,GTuplesList,RangedData-method Man page
subsetByOverlaps,GTuplesList,RangesList-method Man page
subsetByOverlaps,RangedData,GTuples-method Man page
subsetByOverlaps,RangedData,GTuplesList-method Man page
subsetByOverlaps,RangesList,GTuples-method Man page
subsetByOverlaps,RangesList,GTuplesList-method Man page
tile,GTuples-method Man page
trim,GTuples-method Man page
tuples Man page
tuples,GTuples-method Man page
tuples,GTuplesList-method Man page
tuples-squeezers Man page
tuples<- Man page
tuples<-,GTuples-method Man page
tuples<-,GTuplesList-method Man page
union,GTuples,GTuples-method Man page
unlist_list_of_GTuples Source code
updateObject,GTuplesList-method Man page
updateObject,GTupless-method Man page
valid.GTuples Source code
valid.GTuples.mcols Source code
valid.GTuples.pos Source code
valid.GTuplesList Source code
valid.GTuplesList.mcols Source code
width,GTuples-method Man page
width,GTuplesList-method Man page
width<-,GTuples-method Man page
width<-,GTuplesList-method Man page
window,GTuples-method Man page
zero_range Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/AllUtilities.R
R/GTuples-class.R
R/GTuples-comparison.R
R/GTuplesList-class.R
R/GenomicTuples.R
R/RcppExports.R
R/coverage-methods.R
R/findOverlaps-methods.R
R/inter-tuple-methods.R
R/intra-tuple-methods.R
R/nearest-methods.R
R/setops-methods.R
R/tile-methods.R
R/zzz.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/GenomicTuplesIntroduction.R
inst/doc/GenomicTuplesIntroduction.Rmd
inst/doc/GenomicTuplesIntroduction.html
man
man/GTuples-class.Rd
man/GTuples-comparison.Rd
man/GTuplesList-class.Rd
man/GenomicTuples-package.Rd
man/findOverlaps-methods.Rd
man/illdefined-methods.Rd
man/intra-tuple-methods.Rd
man/nearest-methods.Rd
man/tuples-squeezers.Rd
src
src/GenomicTuples_init.c
src/IPD.cpp
src/RcppExports.cpp
src/allTuplesSorted.cpp
src/pcompareGTuples.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/helper-make-test-data.R
tests/testthat/test-AllUtilities.R
tests/testthat/test-GTuples-class.R
tests/testthat/test-GTuples-comparison.R
tests/testthat/test-GTuplesList-class.R
tests/testthat/test-coverage-methods.R
tests/testthat/test-findOverlaps-methods.R
tests/testthat/test-inter-tuple-methods.R
tests/testthat/test-intra-tuple-methods.R
tests/testthat/test-nearest-methods.R
tests/testthat/test-setops-methods.R
tests/testthat/test-tile-methods.R
vignettes
vignettes/GenomicTuplesIntroduction.Rmd
GenomicTuples documentation built on May 20, 2017, 10:22 p.m.