Introduction | Install and load the package | The Seqinfo constructor | Seqinfo accessors | Operations on Seqinfo objects | Subset by seqnames | Rename, drop, add and/or reorder the sequences | Merge Seqinfo objects | Seqinfo objects as parts of higher-level objects | Session information
Package: Seqinfo 1.3.0
Hervé Pagès
Seqinfo: A simple S4 class for storing basic information about a collection of genomic sequences
The Seqinfo class stores the names, lengths, circularity flags, and genomes for a particular collection of sequences. These sequences are typically the chromosomes and/or scaffolds of a specific genome assembly of a given organism. Seqinfo objects are rarely used as standalone objects. Instead, they are used as part of higher-level objects to represent their seqinfo() component. Examples of such higher-level objects are GRanges, RangedSummarizedExperiment, VCF, GAlignments, etc... defined in other Bioconductor infrastructure packages.
Authors:
Seqinfo_1.3.0.tar.gz
Seqinfo_1.3.0.zip(r-4.7)Seqinfo_1.3.0.zip(r-4.6)Seqinfo_1.3.0.zip(r-4.5)
Seqinfo_1.3.0.tgz(r-4.6-any)Seqinfo_1.3.0.tgz(r-4.5-any)
Seqinfo_1.3.0.tar.gz(r-4.7-any)Seqinfo_1.3.0.tar.gz(r-4.6-any)
Seqinfo_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Seqinfo/json (API)
| # Install 'Seqinfo' in R: |
| install.packages('Seqinfo', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/seqinfo/issues
On BioConductor:Seqinfo-1.3.0(bioc 3.24)Seqinfo-1.2.0(bioc 3.23)
infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationbioconductor-packagecore-package
Last updated from:0dcd005b4f. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 240 | ||
| linux-devel-x86_64 | NOTE | 350 | ||
| source / vignettes | OK | 335 | ||
| linux-release-x86_64 | NOTE | 340 | ||
| macos-release-arm64 | NOTE | 201 | ||
| macos-oldrel-arm64 | NOTE | 232 | ||
| windows-devel | NOTE | 214 | ||
| windows-release | NOTE | 220 | ||
| windows-oldrel | NOTE | 216 | ||
| wasm-release | OK | 268 |
Exports:as.data.frameas.data.frame.SeqinfobsgenomeNamecheckCompatibleSeqinfocommonNamegenomegenome<-GenomeDescriptionintersectisCircularisCircular<-mergemerge.SeqinfoorderSeqlevelsorganismproviderproviderVersionrankSeqlevelsreleaseDaterestoreSeqlevelsseqinfoSeqinfoseqinfo<-seqlengthsseqlengths<-seqlevelsseqlevels<-seqlevels0seqlevelsInUseseqnamesseqnames<-showsortSeqlevelssummarysummary.Seqinfoupdateupdate.SeqinfoupdateObject
Dependencies:BiocGenericsgenericsIRangesS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| GenomeDescription objects | bsgenomeName bsgenomeName,GenomeDescription-method class:GenomeDescription commonName commonName,GenomeDescription-method GenomeDescription GenomeDescription-class organism organism,GenomeDescription-method provider provider,GenomeDescription-method providerVersion providerVersion,GenomeDescription-method releaseDate releaseDate,GenomeDescription-method seqinfo,GenomeDescription-method seqnames,GenomeDescription-method show,GenomeDescription-method species species,GenomeDescription-method |
| Assign sequence IDs to sequence names | orderSeqlevels rankSeqlevels |
| Accessing/modifying sequence information | genome genome,ANY-method genome<- genome<-,ANY-method isCircular isCircular,ANY-method isCircular<- isCircular<-,ANY-method restoreSeqlevels seqinfo seqinfo<- seqlengths seqlengths,ANY-method seqlengths<- seqlengths<-,ANY-method seqlevels seqlevels,ANY-method seqlevels0 seqlevels<- seqlevels<-,ANY-method seqnames seqnames<- |
| Seqinfo objects | as.data.frame,Seqinfo-method as.data.frame.Seqinfo checkCompatibleSeqinfo class:Seqinfo coerce,data.frame,Seqinfo-method coerce,DataFrame,Seqinfo-method genome,Seqinfo-method genome<-,Seqinfo-method intersect,Seqinfo,Seqinfo-method isCircular,Seqinfo-method isCircular<-,Seqinfo-method length,Seqinfo-method merge,missing,Seqinfo-method merge,NULL,Seqinfo-method merge,Seqinfo,missing-method merge,Seqinfo,NULL-method merge,Seqinfo,Seqinfo-method merge.Seqinfo names,Seqinfo-method names<-,Seqinfo-method Seqinfo Seqinfo-class seqlengths,Seqinfo-method seqlengths<-,Seqinfo-method seqlevels,Seqinfo-method seqlevels<-,Seqinfo-method seqnames,Seqinfo-method seqnames<-,Seqinfo-method show,Seqinfo-method summary,Seqinfo-method summary.Seqinfo update,Seqinfo-method update.Seqinfo updateObject,Seqinfo-method [,Seqinfo-method |
| Get the sequence levels in use | seqlevelsInUse seqlevelsInUse,CompressedList-method seqlevelsInUse,Vector-method |
| Sort the sequence levels of an object | sortSeqlevels sortSeqlevels,ANY-method sortSeqlevels,character-method |
