Package: GenomicTuples 1.39.0

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-1.39.0(bioc 3.20)GenomicTuples-1.38.0(bioc 3.19)

bioconductor-package

44 exports 1.00 score 19 dependencies

Last updated 2 months agofrom:9a14fe7543

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:askpass BiocGenerics curl data.table GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite mime openssl R6 Rcpp S4Vectors sys UCSC.utils XVector zlibbioc

GenomicTuples: Classes and Methods

Peter Hickey

Rendered fromGenomicTuplesIntroduction.Rmdusingknitr::rmarkdownon Jun 30 2024.

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
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