character vector: strings that are usually circular chromosomes

Description

The DEFAULT_CIRC_SEQS character vector contains strings that are normally used by major repositories as the names of chromosomes that are typically circular, it is available as a convenience so that users can us it as a default value for circ_seqs arguments, and append to it as needed.

Usage

DEFAULT_CIRC_SEQS

See Also

makeTxDbFromUCSC, makeTxDbFromBiomart

Examples

DEFAULT_CIRC_SEQS

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(GenomicFeatures)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/GenomicFeatures/DEFAULT_CIRC_SEQS.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DEFAULT_CIRC_SEQS
> ### Title: character vector: strings that are usually circular chromosomes
> ### Aliases: DEFAULT_CIRC_SEQS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> DEFAULT_CIRC_SEQS
 [1] "chrM"                      "MT"                       
 [3] "MtDNA"                     "mit"                      
 [5] "Mito"                      "mitochondrion"            
 [7] "dmel_mitochondrion_genome" "Pltd"                     
 [9] "ChrC"                      "Pt"                       
[11] "chloroplast"               "Chloro"                   
[13] "2micron"                   "2-micron"                 
[15] "2uM"                      
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>