Last data update: 2014.03.03

 R: Find available/installed genomes
available.genomesR Documentation

Find available/installed genomes

Description

available.genomes gets the list of BSgenome data packages that are available in the Bioconductor repositories for your version of R/Bioconductor.

installed.genomes gets the list of BSgenome data packages that are currently installed on your system.

getBSgenome searchs the installed BSgenome data packages for the specified genome and returns it as a BSgenome object.

Usage

available.genomes(splitNameParts=FALSE, type=getOption("pkgType"))

installed.genomes(splitNameParts=FALSE)

getBSgenome(genome, masked=FALSE)

Arguments

splitNameParts

Whether to split or not the package names in parts. In that case the result is returned in a data frame with 5 columns.

type

Character string indicating the type of package ("source", "mac.binary" or "win.binary") to look for.

genome

A BSgenome object, or the full name of an installed BSgenome data package, or a short string specifying a genome assembly (a.k.a. provider version) that refers unambiguously to an installed BSgenome data package.

masked

TRUE or FALSE. Whether to search for the masked BSgenome object (i.e. the object that contains the masked sequences) or not (the default).

Details

A BSgenome data package contains the full genome sequences for a given organism.

Its name typically has 4 parts (5 parts if it's a masked BSgenome data package i.e. if it contains masked sequences) separated by a dot e.g. BSgenome.Mmusculus.UCSC.mm10 or BSgenome.Mmusculus.UCSC.mm10.masked:

  1. The 1st part is always BSgenome.

  2. The 2nd part is the name of the organism in abbreviated form e.g. Mmusculus, Hsapiens, Celegans, Scerevisiae, Ecoli, etc...

  3. The 3rd part is the name of the organisation who provided the genome sequences. We formally refer to it as the provider of the genome. E.g. UCSC, NCBI, TAIR, etc...

  4. The 4th part is the release string or number used by this organisation for this particular genome assembly. We formally refer to it as the provider version of the genome. E.g. hg38, GRCh38, hg19, mm10, susScr3, etc...

  5. If the package contains masked sequences, its name has the .masked suffix added to it, which is typically the 5th part.

A BSgenome data package contains a single top-level object (a BSgenome object) named like the package itself that can be used to access the genome sequences.

Value

For available.genomes and installed.genomes: by default (i.e. if splitNameParts=FALSE), a character vector containing the names of the BSgenome data packages that are available (for available.genomes) or currently installed (for installed.genomes). If splitNameParts=TRUE, the list of packages is returned in a data frame with one row per package and the following columns: pkgname (character), organism (factor), provider (factor), provider_version (character), and masked (logical).

For getBSgenome: the BSgenome object containing the sequences for the specified genome. Or an error if the object cannot be found in the BSgenome data packages currently installed.

Author(s)

H. Pag<c3><83><c2><a8>s

See Also

  • BSgenome objects.

  • available.packages.

Examples

## ---------------------------------------------------------------------
## available.genomes() and installed.genomes()
## ---------------------------------------------------------------------

# What genomes are currently installed:
installed.genomes()

# What genomes are available:
available.genomes()

# Split the package names in parts:
av_gen <- available.genomes(splitNameParts=TRUE)
table(av_gen$organism)
table(av_gen$provider)

# Make your choice and install with:
library(BiocInstaller)
biocLite("BSgenome.Scerevisiae.UCSC.sacCer1")

# Have a coffee 8-)

# Load the package and display the index of sequences for this genome:
library(BSgenome.Scerevisiae.UCSC.sacCer1)
Scerevisiae  # same as BSgenome.Scerevisiae.UCSC.sacCer1

## ---------------------------------------------------------------------
## getBSgenome()
## ---------------------------------------------------------------------

## Specify the full name of an installed BSgenome data package:
genome <- getBSgenome("BSgenome.Celegans.UCSC.ce2")
genome

## Specify a genome assembly (a.k.a. provider version):
genome <- getBSgenome("hg38")
class(genome)  # BSgenome object
providerVersion(genome)
genome$chrM

genome <- getBSgenome("hg38", masked=TRUE)
class(genome)  # MaskedBSgenome object
providerVersion(genome)
genome$chr22

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BSgenome)
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: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BSgenome/available.genomes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: available.genomes
> ### Title: Find available/installed genomes
> ### Aliases: available.genomes installed.genomes getBSgenome
> ### Keywords: manip
> 
> ### ** Examples
> 
> ## ---------------------------------------------------------------------
> ## available.genomes() and installed.genomes()
> ## ---------------------------------------------------------------------
> 
> # What genomes are currently installed:
> installed.genomes()
 [1] "BSgenome.Alyrata.JGI.v1"                  
 [2] "BSgenome.Amellifera.BeeBase.assembly4"    
 [3] "BSgenome.Amellifera.UCSC.apiMel2"         
 [4] "BSgenome.Amellifera.UCSC.apiMel2.masked"  
 [5] "BSgenome.Athaliana.TAIR.04232008"         
 [6] "BSgenome.Athaliana.TAIR.TAIR9"            
 [7] "BSgenome.Btaurus.UCSC.bosTau3"            
 [8] "BSgenome.Btaurus.UCSC.bosTau3.masked"     
 [9] "BSgenome.Btaurus.UCSC.bosTau4"            
[10] "BSgenome.Btaurus.UCSC.bosTau4.masked"     
[11] "BSgenome.Btaurus.UCSC.bosTau6"            
[12] "BSgenome.Btaurus.UCSC.bosTau6.masked"     
[13] "BSgenome.Btaurus.UCSC.bosTau8"            
[14] "BSgenome.Celegans.UCSC.ce10"              
[15] "BSgenome.Celegans.UCSC.ce11"              
[16] "BSgenome.Celegans.UCSC.ce2"               
[17] "BSgenome.Celegans.UCSC.ce6"               
[18] "BSgenome.Cfamiliaris.UCSC.canFam2"        
[19] "BSgenome.Cfamiliaris.UCSC.canFam2.masked" 
[20] "BSgenome.Cfamiliaris.UCSC.canFam3"        
[21] "BSgenome.Cfamiliaris.UCSC.canFam3.masked" 
[22] "BSgenome.Dmelanogaster.UCSC.dm2"          
[23] "BSgenome.Dmelanogaster.UCSC.dm2.masked"   
[24] "BSgenome.Dmelanogaster.UCSC.dm3"          
[25] "BSgenome.Dmelanogaster.UCSC.dm3.masked"   
[26] "BSgenome.Dmelanogaster.UCSC.dm6"          
[27] "BSgenome.Drerio.UCSC.danRer10"            
[28] "BSgenome.Drerio.UCSC.danRer5"             
[29] "BSgenome.Drerio.UCSC.danRer5.masked"      
[30] "BSgenome.Drerio.UCSC.danRer6"             
[31] "BSgenome.Drerio.UCSC.danRer6.masked"      
[32] "BSgenome.Drerio.UCSC.danRer7"             
[33] "BSgenome.Drerio.UCSC.danRer7.masked"      
[34] "BSgenome.Ecoli.NCBI.20080805"             
[35] "BSgenome.Gaculeatus.UCSC.gasAcu1"         
[36] "BSgenome.Gaculeatus.UCSC.gasAcu1.masked"  
[37] "BSgenome.Ggallus.UCSC.galGal3"            
[38] "BSgenome.Ggallus.UCSC.galGal3.masked"     
[39] "BSgenome.Ggallus.UCSC.galGal4"            
[40] "BSgenome.Ggallus.UCSC.galGal4.masked"     
[41] "BSgenome.Hsapiens.1000genomes.hs37d5"     
[42] "BSgenome.Hsapiens.NCBI.GRCh38"            
[43] "BSgenome.Hsapiens.UCSC.hg17"              
[44] "BSgenome.Hsapiens.UCSC.hg17.masked"       
[45] "BSgenome.Hsapiens.UCSC.hg18"              
[46] "BSgenome.Hsapiens.UCSC.hg18.masked"       
[47] "BSgenome.Hsapiens.UCSC.hg19"              
[48] "BSgenome.Hsapiens.UCSC.hg19.masked"       
[49] "BSgenome.Hsapiens.UCSC.hg38"              
[50] "BSgenome.Hsapiens.UCSC.hg38.masked"       
[51] "BSgenome.Mfascicularis.NCBI.5.0"          
[52] "BSgenome.Mfuro.UCSC.musFur1"              
[53] "BSgenome.Mmulatta.UCSC.rheMac2"           
[54] "BSgenome.Mmulatta.UCSC.rheMac2.masked"    
[55] "BSgenome.Mmulatta.UCSC.rheMac3"           
[56] "BSgenome.Mmulatta.UCSC.rheMac3.masked"    
[57] "BSgenome.Mmusculus.UCSC.mm10"             
[58] "BSgenome.Mmusculus.UCSC.mm10.masked"      
[59] "BSgenome.Mmusculus.UCSC.mm8"              
[60] "BSgenome.Mmusculus.UCSC.mm8.masked"       
[61] "BSgenome.Mmusculus.UCSC.mm9"              
[62] "BSgenome.Mmusculus.UCSC.mm9.masked"       
[63] "BSgenome.Osativa.MSU.MSU7"                
[64] "BSgenome.Ptroglodytes.UCSC.panTro2"       
[65] "BSgenome.Ptroglodytes.UCSC.panTro2.masked"
[66] "BSgenome.Ptroglodytes.UCSC.panTro3"       
[67] "BSgenome.Ptroglodytes.UCSC.panTro3.masked"
[68] "BSgenome.Rnorvegicus.UCSC.rn4"            
[69] "BSgenome.Rnorvegicus.UCSC.rn4.masked"     
[70] "BSgenome.Rnorvegicus.UCSC.rn5"            
[71] "BSgenome.Rnorvegicus.UCSC.rn5.masked"     
[72] "BSgenome.Rnorvegicus.UCSC.rn6"            
[73] "BSgenome.Scerevisiae.UCSC.sacCer1"        
[74] "BSgenome.Scerevisiae.UCSC.sacCer2"        
[75] "BSgenome.Scerevisiae.UCSC.sacCer3"        
[76] "BSgenome.Sscrofa.UCSC.susScr3"            
[77] "BSgenome.Sscrofa.UCSC.susScr3.masked"     
[78] "BSgenome.Tgondii.ToxoDB.7.0"              
[79] "BSgenome.Tguttata.UCSC.taeGut1"           
[80] "BSgenome.Tguttata.UCSC.taeGut1.masked"    
[81] "BSgenome.Tguttata.UCSC.taeGut2"           
[82] "BSgenome.Vvinifera.URGI.IGGP12Xv0"        
[83] "BSgenome.Vvinifera.URGI.IGGP12Xv2"        
[84] "BSgenome.Vvinifera.URGI.IGGP8X"           
> 
> # What genomes are available:
> available.genomes()
 [1] "BSgenome.Alyrata.JGI.v1"                  
 [2] "BSgenome.Amellifera.BeeBase.assembly4"    
 [3] "BSgenome.Amellifera.UCSC.apiMel2"         
 [4] "BSgenome.Amellifera.UCSC.apiMel2.masked"  
 [5] "BSgenome.Athaliana.TAIR.04232008"         
 [6] "BSgenome.Athaliana.TAIR.TAIR9"            
 [7] "BSgenome.Btaurus.UCSC.bosTau3"            
 [8] "BSgenome.Btaurus.UCSC.bosTau3.masked"     
 [9] "BSgenome.Btaurus.UCSC.bosTau4"            
[10] "BSgenome.Btaurus.UCSC.bosTau4.masked"     
[11] "BSgenome.Btaurus.UCSC.bosTau6"            
[12] "BSgenome.Btaurus.UCSC.bosTau6.masked"     
[13] "BSgenome.Btaurus.UCSC.bosTau8"            
[14] "BSgenome.Celegans.UCSC.ce10"              
[15] "BSgenome.Celegans.UCSC.ce11"              
[16] "BSgenome.Celegans.UCSC.ce2"               
[17] "BSgenome.Celegans.UCSC.ce6"               
[18] "BSgenome.Cfamiliaris.UCSC.canFam2"        
[19] "BSgenome.Cfamiliaris.UCSC.canFam2.masked" 
[20] "BSgenome.Cfamiliaris.UCSC.canFam3"        
[21] "BSgenome.Cfamiliaris.UCSC.canFam3.masked" 
[22] "BSgenome.Dmelanogaster.UCSC.dm2"          
[23] "BSgenome.Dmelanogaster.UCSC.dm2.masked"   
[24] "BSgenome.Dmelanogaster.UCSC.dm3"          
[25] "BSgenome.Dmelanogaster.UCSC.dm3.masked"   
[26] "BSgenome.Dmelanogaster.UCSC.dm6"          
[27] "BSgenome.Drerio.UCSC.danRer10"            
[28] "BSgenome.Drerio.UCSC.danRer5"             
[29] "BSgenome.Drerio.UCSC.danRer5.masked"      
[30] "BSgenome.Drerio.UCSC.danRer6"             
[31] "BSgenome.Drerio.UCSC.danRer6.masked"      
[32] "BSgenome.Drerio.UCSC.danRer7"             
[33] "BSgenome.Drerio.UCSC.danRer7.masked"      
[34] "BSgenome.Ecoli.NCBI.20080805"             
[35] "BSgenome.Gaculeatus.UCSC.gasAcu1"         
[36] "BSgenome.Gaculeatus.UCSC.gasAcu1.masked"  
[37] "BSgenome.Ggallus.UCSC.galGal3"            
[38] "BSgenome.Ggallus.UCSC.galGal3.masked"     
[39] "BSgenome.Ggallus.UCSC.galGal4"            
[40] "BSgenome.Ggallus.UCSC.galGal4.masked"     
[41] "BSgenome.Hsapiens.1000genomes.hs37d5"     
[42] "BSgenome.Hsapiens.NCBI.GRCh38"            
[43] "BSgenome.Hsapiens.UCSC.hg17"              
[44] "BSgenome.Hsapiens.UCSC.hg17.masked"       
[45] "BSgenome.Hsapiens.UCSC.hg18"              
[46] "BSgenome.Hsapiens.UCSC.hg18.masked"       
[47] "BSgenome.Hsapiens.UCSC.hg19"              
[48] "BSgenome.Hsapiens.UCSC.hg19.masked"       
[49] "BSgenome.Hsapiens.UCSC.hg38"              
[50] "BSgenome.Hsapiens.UCSC.hg38.masked"       
[51] "BSgenome.Mfascicularis.NCBI.5.0"          
[52] "BSgenome.Mfuro.UCSC.musFur1"              
[53] "BSgenome.Mmulatta.UCSC.rheMac2"           
[54] "BSgenome.Mmulatta.UCSC.rheMac2.masked"    
[55] "BSgenome.Mmulatta.UCSC.rheMac3"           
[56] "BSgenome.Mmulatta.UCSC.rheMac3.masked"    
[57] "BSgenome.Mmusculus.UCSC.mm10"             
[58] "BSgenome.Mmusculus.UCSC.mm10.masked"      
[59] "BSgenome.Mmusculus.UCSC.mm8"              
[60] "BSgenome.Mmusculus.UCSC.mm8.masked"       
[61] "BSgenome.Mmusculus.UCSC.mm9"              
[62] "BSgenome.Mmusculus.UCSC.mm9.masked"       
[63] "BSgenome.Osativa.MSU.MSU7"                
[64] "BSgenome.Ptroglodytes.UCSC.panTro2"       
[65] "BSgenome.Ptroglodytes.UCSC.panTro2.masked"
[66] "BSgenome.Ptroglodytes.UCSC.panTro3"       
[67] "BSgenome.Ptroglodytes.UCSC.panTro3.masked"
[68] "BSgenome.Rnorvegicus.UCSC.rn4"            
[69] "BSgenome.Rnorvegicus.UCSC.rn4.masked"     
[70] "BSgenome.Rnorvegicus.UCSC.rn5"            
[71] "BSgenome.Rnorvegicus.UCSC.rn5.masked"     
[72] "BSgenome.Rnorvegicus.UCSC.rn6"            
[73] "BSgenome.Scerevisiae.UCSC.sacCer1"        
[74] "BSgenome.Scerevisiae.UCSC.sacCer2"        
[75] "BSgenome.Scerevisiae.UCSC.sacCer3"        
[76] "BSgenome.Sscrofa.UCSC.susScr3"            
[77] "BSgenome.Sscrofa.UCSC.susScr3.masked"     
[78] "BSgenome.Tgondii.ToxoDB.7.0"              
[79] "BSgenome.Tguttata.UCSC.taeGut1"           
[80] "BSgenome.Tguttata.UCSC.taeGut1.masked"    
[81] "BSgenome.Tguttata.UCSC.taeGut2"           
[82] "BSgenome.Vvinifera.URGI.IGGP12Xv0"        
[83] "BSgenome.Vvinifera.URGI.IGGP12Xv2"        
[84] "BSgenome.Vvinifera.URGI.IGGP8X"           
> 
> # Split the package names in parts:
> av_gen <- available.genomes(splitNameParts=TRUE)
> table(av_gen$organism)

      Alyrata    Amellifera     Athaliana       Btaurus      Celegans 
            1             3             2             7             4 
  Cfamiliaris Dmelanogaster        Drerio         Ecoli    Gaculeatus 
            4             5             7             1             2 
      Ggallus      Hsapiens Mfascicularis         Mfuro      Mmulatta 
            4            10             1             1             4 
    Mmusculus       Osativa  Ptroglodytes   Rnorvegicus   Scerevisiae 
            6             1             4             5             3 
      Sscrofa       Tgondii      Tguttata     Vvinifera 
            2             1             3             3 
> table(av_gen$provider)

1000genomes     BeeBase         JGI         MSU        NCBI        TAIR 
          1           1           1           1           3           2 
     ToxoDB        UCSC        URGI 
          1          71           3 
> 
> # Make your choice and install with:
> library(BiocInstaller)
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
> biocLite("BSgenome.Scerevisiae.UCSC.sacCer1")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.3), R 3.3.1 (2016-06-21).
Installing package(s) 'BSgenome.Scerevisiae.UCSC.sacCer1'
trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz'
Content type 'application/x-gzip' length 2967322 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package 'BSgenome.Scerevisiae.UCSC.sacCer1' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'BSgenome.Scerevisiae.UCSC.sacCer1'
    finding HTML links ... done
    package                                 html  
Rd warning: /tmp/RtmpWYuq93/R.INSTALL7f7d9d12805/BSgenome.Scerevisiae.UCSC.sacCer1/man/package.Rd:33: missing file link 'BSgenome'
Rd warning: /tmp/RtmpWYuq93/R.INSTALL7f7d9d12805/BSgenome.Scerevisiae.UCSC.sacCer1/man/package.Rd:36: missing file link 'DNAString'
** building package indices
** testing if installed package can be loaded
* DONE (BSgenome.Scerevisiae.UCSC.sacCer1)
Making 'packages.html' ... done

The downloaded source packages are in
	'/tmp/RtmpqNU0j4/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'AdaptGauss', 'BAS', 'BalancedSampling', 'BatchQC',
  'BayesTreePrior', 'COCONUT', 'ChannelAttribution', 'Comp2ROC', 'CompGO',
  'DAMisc', 'DAPAR', 'DEoptimR', 'DIFtree', 'DeLorean', 'ECctmc',
  'EnsemblePCReg', 'FSelector', 'GGally', 'GSODR', 'Grace', 'IRTpp',
  'InspectChangepoint', 'IsoplotR', 'MCI', 'MNM', 'ModelMap', 'PResiduals',
  'PoisNor', 'Prostar', 'RForcecom', 'RNeXML', 'RTriangle',
  'RandomFieldsUtils', 'RcppShark', 'Renext', 'Rtsne', 'SIDES', 'SKAT',
  'SNPhood', 'STB', 'Segmentor3IsBack', 'Sequential', 'SubVis', 'UNCLES',
  'VIM', 'VariantFiltering', 'XBRL', 'adespatial', 'astsa', 'batchmeans',
  'bayesmeta', 'brms', 'clusterProfiler', 'condvis', 'copCAR', 'crayon',
  'crunch', 'data.tree', 'dbmss', 'emojifont', 'enpls', 'ensembldb', 'evclass',
  'evoper', 'ezsummary', 'fcros', 'fitdistrplus', 'flowStats', 'fmrs',
  'future', 'fuzzyjoin', 'gazepath', 'generalCorr', 'geomnet', 'gets',
  'ggenealogy', 'ggiraph', 'ggmcmc', 'ggtree', 'gramEvol', 'graphicalVAR',
  'heemod', 'hergm', 'httr', 'hypothesisr', 'invgamma', 'isingLenzMC',
  'jetset', 'jsonlite', 'kernscr', 'lfstat', 'limma', 'manifestoR',
  'markovchain', 'meta4diag', 'metaheur', 'miscFuncs', 'mkin', 'mlVAR',
  'mokken', 'networkD3', 'nparACT', 'planor', 'pomp', 'psych', 'qgraph',
  'qtlcharts', 'ramps', 'randNames', 'rankFD', 'recmap', 'resumer', 'rts',
  'sensitivity', 'sn', 'sommer', 'spatsurv', 'ssa', 'stpm', 'sudokuAlt',
  'survSNP', 'surveyplanning', 'synthACS', 'tibble', 'tm.plugin.lexisnexis',
  'useful', 'vipor', 'vmsbase', 'wgaim'
> 
> # Have a coffee 8-)
> 
> # Load the package and display the index of sequences for this genome:
> library(BSgenome.Scerevisiae.UCSC.sacCer1)
> Scerevisiae  # same as BSgenome.Scerevisiae.UCSC.sacCer1
Yeast genome:
# organism: Saccharomyces cerevisiae (Yeast)
# provider: UCSC
# provider version: sacCer1
# release date: Oct. 2003
# release name: SGD 1 Oct 2003 sequence
# 17 sequences:
#   chr1  chr2  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chr10 chr11 chr12
#   chr13 chr14 chr15 chr16 chrM                                           
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> 
> ## ---------------------------------------------------------------------
> ## getBSgenome()
> ## ---------------------------------------------------------------------
> 
> ## Specify the full name of an installed BSgenome data package:
> genome <- getBSgenome("BSgenome.Celegans.UCSC.ce2")
> genome
Worm genome:
# organism: Caenorhabditis elegans (Worm)
# provider: UCSC
# provider version: ce2
# release date: Mar. 2004
# release name: WormBase v. WS120
# 7 sequences:
#   chrI   chrII  chrIII chrIV  chrV   chrX   chrM                              
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> 
> ## Specify a genome assembly (a.k.a. provider version):
> genome <- getBSgenome("hg38")
> class(genome)  # BSgenome object
[1] "BSgenome"
attr(,"package")
[1] "BSgenome"
> providerVersion(genome)
[1] "hg38"
> genome$chrM
  16569-letter "DNAString" instance
seq: GATCACAGGTCTATCACCCTATTAACCACTCACGGG...AGCCCACACGTTCCCCTTAAATAAGACATCACGATG
> 
> genome <- getBSgenome("hg38", masked=TRUE)
> class(genome)  # MaskedBSgenome object
[1] "MaskedBSgenome"
attr(,"package")
[1] "BSgenome"
> providerVersion(genome)
[1] "hg38"
> genome$chr22
  50818468-letter "MaskedDNAString" instance (# for masking)
seq: ####################################...####################################
masks:
  maskedwidth  maskedratio active names                               desc
1    11658686 2.294183e-01   TRUE AGAPS                      assembly gaps
2           5 9.838943e-08   TRUE   AMB           intra-contig ambiguities
3    20908105 4.114273e-01  FALSE    RM                       RepeatMasker
4      420832 8.281084e-03  FALSE   TRF Tandem Repeats Finder [period<=12]
all masks together:
  maskedwidth maskedratio
     32606167   0.6416204
all active masks together:
  maskedwidth maskedratio
     11658691   0.2294184
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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