Package: GenomicTuples 1.47.0

Peter Hickey

GenomicTuples: Representation and Manipulation of Genomic Tuples

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.

Authors:Peter Hickey [aut, cre], Marcin Cieslik [ctb], Hervé Pagès [ctb]

# Install 'GenomicTuples' in R:

install.packages('GenomicTuples', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/petehaitch/genomictuples/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:GenomicTuples-1.47.0(bioc 3.24)GenomicTuples-1.46.0(bioc 3.23)

infrastructure datarepresentation sequencing cpp

5.57 score 5 stars 7 scripts 44 exports 8 dependencies

Last updated from:63054408c8. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	175
linux-devel-arm64	NOTE	223
linux-devel-x86_64	NOTE	255
source / vignettes	OK	225
linux-release-arm64	NOTE	218
linux-release-x86_64	NOTE	278
macos-release-arm64	NOTE	183
macos-release-x86_64	NOTE	319
macos-oldrel-arm64	NOTE	171
macos-oldrel-x86_64	NOTE	408
windows-devel	NOTE	178
windows-release	NOTE	204
windows-oldrel	NOTE	206
wasm-release	OK	170

Exports:as.data.frame countOverlaps coverage disjoin disjointBins duplicated duplicated.GTuples findOverlaps flank gaps granges gtlist gtuples GTuples GTuplesList intersect IPD is.unsorted isDisjoint match narrow Ops order pcompare pgap pintersect promoters psetdiff punion reduce relistToClass resize restrict selfmatch setdiff shift show size sort sort.GTuples tile tuples tuples<-union

Dependencies:BiocGenerics data.table generics GenomicRanges IRanges Rcpp S4Vectors Seqinfo

GenomicTuples: Classes and Methods

Introduction | What is a genomic tuple? | When might you need a genomic tuple? | GTuples | GTuples methods | Basic GTuples accessors | Splitting and combining GTuples objects} | Subsetting GTuples objects | Basic tuple operations for GTuples objects | Intra-tuple operations | Inter-tuple operations | Interval set operations for GTuples objects | Additional methods unique to GTuples | Implementation details | GTuplesList | GTuplesList methods | Basic GTuplesList accessors} | Combining GTuplesList objects | Subsetting GTuplesList objects | Basic tuple operations for GTuplesList objects | Interval set operations for GTuplesList objects | Looping over GTuplesList objects | Additional methods unique to GTuplesList | findOverlaps-based methods | Definition of overlapping genomic tuples | Definition of overlapping genomic tuples and ranges | Examples | Comparison of genomic tuples | Definition of comparison methods for genomic tuples | Acknowledgements | Session info | References

Rendered fromGenomicTuplesIntroduction.Rmdusingknitr::rmarkdown

Last update: 2016-05-26
Started: 2015-02-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Representation and manipulation of genomic tuples.	GenomicTuples-package GenomicTuples
Finding overlapping genomic tuples	countOverlaps countOverlaps,GTuples,GTuples-method findOverlaps findOverlaps,GTuples,GTuples-method findOverlaps-methods overlapsAny overlapsAny,GTuples,GTuples-method subsetByOverlaps subsetByOverlaps,GTuples,GTuples-method
GTuples objects	$,GTuples-method $<-,GTuples,numeric-method as.character,GTuples-method as.data.frame,GTuples-method as.factor,GTuples-method c,GTuples-method class:GTuples coerce,GRanges,GTuples-method elementMetadata<-,GTuples-method end,GTuples-method end<-,GTuples-method granges,GTuples-method GTuples GTuples-class IPD IPD,GTuples-method length,GTuples-method names,GTuples-method names<-,GTuples-method ranges,GTuples-method ranges<-,GTuples-method score,GTuples-method score<-,GTuples-method seqinfo,GTuples-method seqinfo<-,GTuples-method seqnames,GTuples-method seqnames<-,GTuples-method show,GTuples-method size size,GTuples-method start,GTuples-method start<-,GTuples-method strand,GTuples-method strand<-,GTuples-method tuples tuples,GTuples-method tuples<- tuples<-,GTuples-method updateObject,GTupless-method width,GTuples-method width<-,GTuples-method window,GTuples-method [,GTuples-method [<-,GTuples-method
Comparing and ordering genomic tuples	duplicated,GTuples-method duplicated.GTuples GTuples-comparison is.unsorted,GTuples-method match,GTuples,GTuples-method order,GTuples-method pcompare,GTuples,GTuples-method rank,GTuples-method selfmatch,GTuples-method sort,GTuples-method sort.GTuples
GTuplesList objects	class:GTuplesList coerce,GTuplesList,data.frame-method coerce,GTuplesList,GRangesList-method coerce,GTuplesList,list-method elementMetadata,GTuplesList-method elementMetadata<-,GTuplesList-method end,GTuplesList-method end<-,GTuplesList-method GTuplesList GTuplesList-class IPD,GTuplesList-method ranges,GTuplesList-method ranges<-,GTuplesList-method relistToClass,GTuples-method score,GTuplesList-method score<-,GTuplesList-method seqinfo,GTuplesList-method seqinfo<-,GTuplesList-method seqnames,GTuplesList-method seqnames<-,GTuplesList-method size,GTuplesList-method start,GTuplesList-method start<-,GTuplesList-method strand,GTuplesList-method strand<-,GTuplesList,ANY-method strand<-,GTuplesList,character-method tuples,GTuplesList-method tuples<-,GTuplesList-method updateObject,GTuplesList-method width,GTuplesList-method width<-,GTuplesList-method [,GTuplesList,ANY-method [<-,GTuplesList,ANY,ANY,ANY-method [[<-,GTuplesList,ANY,ANY,ANY-method
Intra-tuple transformations of a GTuples or GTuplesLists object	intra-tuple-methods shift shift,GTuples-method shift,GTuplesList-method trim,GTuples-method
Finding the nearest genomic tuple/range neighbour	distance,GTuples,GTuples-method distanceToNearest,GTuples,GTuples-method distanceToNearest,GTuples,missing-method follow,GTuples,GTuples-method follow,GTuples,missing-method nearest,GTuples,GTuples-method nearest,GTuples,missing-method nearest-methods precede,GTuples,GTuples-method precede,GTuples,missing-method
Squeeze the tuples out of a tuples-based object	gtlist gtuples tuples-squeezers
Undefined methods	coverage,GTuples-method coverage,GTuplesList-method disjoin,GTuples-method disjoin,GTuplesList-method disjointBins,GTuples-method flank,GTuples-method flank,GTuplesList-method gaps,GTuples-method intersect,GTuples,GTuples-method isDisjoint,GTuples-method isDisjoint,GTuplesList-method narrow narrow,GTuples-method Ops,GTuples,numeric-method pgap,GTuples,GTuples-method pintersect,GTuples,GTuples-method pintersect,GTuples,GTuplesList-method pintersect,GTuplesList,GTuples-method pintersect,GTuplesList,GTuplesList-method promoters,GTuples-method promoters,GTuplesList-method psetdiff,GTuples,GTuples-method psetdiff,GTuples,GTuplesList-method psetdiff,GTuplesList,GTuplesList-method punion,GTuples,GTuples-method punion,GTuples,GTuplesList-method punion,GTuplesList,GTuples-method range,GTuples-method range,GTuplesList-method reduce,GTuples-method reduce,GTuplesList-method replaceROWS,NULL-method resize,GTuples-method resize,GTuplesList-method restrict,GTuplesList-method setdiff,GTuples,GTuples-method tile,GTuples-method union,GTuples,GTuples-method