Last data update: 2014.03.03

 R: BSgenomeViews objects
BSgenomeViews-classR Documentation

BSgenomeViews objects

Description

The BSgenomeViews class is a container for storing a set of genomic positions on a BSgenome object, called the "subject" in this context.

Usage

## Constructor
## ------------

BSgenomeViews(subject, granges)

## Accessors
## ---------

## S4 method for signature 'BSgenomeViews'
subject(x)
## S4 method for signature 'BSgenomeViews'
granges(x, use.mcols=FALSE)

## S4 method for signature 'BSgenomeViews'
length(x)
## S4 method for signature 'BSgenomeViews'
names(x)
## S4 method for signature 'BSgenomeViews'
seqnames(x)
## S4 method for signature 'BSgenomeViews'
start(x)
## S4 method for signature 'BSgenomeViews'
end(x)
## S4 method for signature 'BSgenomeViews'
width(x)
## S4 method for signature 'BSgenomeViews'
strand(x)
## S4 method for signature 'BSgenomeViews'
ranges(x, use.mcols=FALSE)
## S4 method for signature 'BSgenomeViews'
elementNROWS(x)
## S4 method for signature 'BSgenomeViews'
seqinfo(x)

## DNAStringSet methods
## --------------------

## S4 method for signature 'BSgenomeViews'
seqtype(x)

## S4 method for signature 'BSgenomeViews'
nchar(x, type="chars", allowNA=FALSE)

## S4 method for signature 'BSgenomeViews'
unlist(x, recursive=TRUE, use.names=TRUE)

## S4 method for signature 'BSgenomeViews'
alphabetFrequency(x, as.prob=FALSE, collapse=FALSE, baseOnly=FALSE)

## S4 method for signature 'BSgenomeViews'
hasOnlyBaseLetters(x)

## S4 method for signature 'BSgenomeViews'
uniqueLetters(x)

## S4 method for signature 'BSgenomeViews'
letterFrequency(x, letters, OR="|", as.prob=FALSE, collapse=FALSE)

## S4 method for signature 'BSgenomeViews'
oligonucleotideFrequency(x, width, step=1,
                         as.prob=FALSE, as.array=FALSE,
                         fast.moving.side="right", with.labels=TRUE, simplify.as="matrix")

## S4 method for signature 'BSgenomeViews'
nucleotideFrequencyAt(x, at, as.prob=FALSE, as.array=TRUE,
                      fast.moving.side="right", with.labels=TRUE)

## S4 method for signature 'BSgenomeViews'
consensusMatrix(x, as.prob=FALSE, shift=0L, width=NULL, baseOnly=FALSE)

## S4 method for signature 'BSgenomeViews'
consensusString(x, ambiguityMap=IUPAC_CODE_MAP, threshold=0.25,
                shift=0L, width=NULL)

Arguments

subject

A BSgenome object or the name of a reference genome specified in a way that is accepted by the getBSgenome function. In that case the corresponding BSgenome data package needs to be already installed (see ?getBSgenome for the details).

granges

A GRanges object containing ranges relative to the genomic sequences stored in subject.

x

A BSgenomeViews object.

use.mcols

TRUE or FALSE (the default). Whether the metadata columns on x (accessible with mcols(x)) should be propagated to the returned object or not.

type, allowNA, recursive, use.names

Ignored.

as.prob, letters, OR, width

See ?alphabetFrequency and ?oligonucleotideFrequency in the Biostrings package.

collapse, baseOnly

See ?alphabetFrequency in the Biostrings package.

step, as.array, fast.moving.side, with.labels, simplify.as, at

See ?oligonucleotideFrequency in the Biostrings package.

shift, ambiguityMap, threshold

See ?consensusMatrix in the Biostrings package.

Constructors

BSgenomeViews(subject, granges): Make a BSgenomeViews object by putting the views specified by granges on top of the genomic sequences stored in subject. See above for how argument subject and granges should be specified.

Views(subject, granges): Equivalent to BSgenomeViews(subject, granges). Provided for convenience.

Accessors

In the code snippets below, x is a BSgenomeViews object.

subject(x): Return the BSgenome object containing the full genomic sequences on top of which the views in x are defined.

granges(x, use.mcols=FALSE): Return the genomic ranges of the views as a GRanges object. These ranges are relative to the genomic sequences stored in subject(x).

length(x): The number of views in x.

names(x): The names of the views in x.

seqnames(x), start(x), end(x), width(x), strand(x): Equivalent to seqnames(granges(x)), start(granges(x)), end(granges(x)), width(granges(x)), strand(granges(x)), respectively.

ranges(x, use.mcols=FALSE): Equivalent to ranges(granges(x, use.mcols), use.mcols).

elementNROWS(x): Equivalent to width(x).

seqinfo(x): Equivalent to seqinfo(subject(x)) and to seqinfo(granges(x)) (both are guaranteed to be the same). See ?seqinfo in the GenomeInfoDb package for more information.

Coercion

In the code snippets below, x is a BSgenomeViews object.

as(x, "DNAStringSet"): Turn x into a DNAStringSet object by extxracting the DNA sequence corresponding to each view. Alternatively as(x, "XStringSet") can be used for this, and is equivalent to as(x, "DNAStringSet").

as.character(x): Equivalent to as.character(as(x, "DNAStringSet")).

as.data.frame(x): Turn x into a data.frame.

Subsetting

x[i]: Select the views specified by i.

x[[i]]: Extract the one view specified by i.

DNAStringSet methods

For convenience, some methods defined for DNAStringSet objects in the Biostrings package can be used directly on a BSgenomeViews object. In that case, everything happens like if the BSgenomeViews object x was turned into a DNAStringSet object (with as(x, "DNAStringSet")) before it's passed to the method for DNAStringSet objects.

At the moment, the list of such methods is: seqtype, nchar,XStringSet-method, unlist,XStringSet-method, alphabetFrequency, hasOnlyBaseLetters, uniqueLetters, letterFrequency, oligonucleotideFrequency, nucleotideFrequencyAt, consensusMatrix, and consensusString.

See the corresponding man page in the Biostrings package for a description of these methods.

Author(s)

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

See Also

  • The BSgenome class.

  • The GRanges class in the GenomicRanges package.

  • The DNAStringSet class in the Biostrings package.

  • The seqinfo and related getters in the GenomeInfoDb package for getting the sequence information stored in an object.

  • TxDb objects in the GenomicFeatures package.

Examples

library(BSgenome.Mmusculus.UCSC.mm10)
genome <- BSgenome.Mmusculus.UCSC.mm10
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
ex <- exons(txdb, columns=c("exon_id", "tx_name", "gene_id"))
v <- Views(genome, ex)
v

subject(v)
granges(v)
seqinfo(v)
as(v, "DNAStringSet")

v10 <- v[1:10]  # select the first 10 views
subject(v10)    # same as subject(v)
granges(v10)
seqinfo(v10)    # same as seqinfo(v)
as(v10, "DNAStringSet")
alphabetFrequency(v10)
alphabetFrequency(v10, collapse=TRUE)

v12 <- v[width(v) <= 12]  # select the views of 12 nucleotides or less
head(as.data.frame(v12))
trinucleotideFrequency(v12, simplify.as="collapsed")

## BSgenomeViews objects are list-like objects. That is, the
## BSgenomeViews class derives from List and typical list/List
## operations (e.g. [[, elementNROWS(), unlist(), elementType(),
## etc...) work on these objects:
is(v12, "List")  # TRUE
v12[[2]]
head(elementNROWS(v12))  # elementNROWS(v) is the same as width(v)
unlist(v12) 
elementType(v12)

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/BSgenomeViews-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSgenomeViews-class
> ### Title: BSgenomeViews objects
> ### Aliases: class:BSgenomeViews BSgenomeViews-class BSgenomeViews
> ###   Views,BSgenome-method subject,BSgenomeViews-method
> ###   granges,BSgenomeViews-method length,BSgenomeViews-method
> ###   names,BSgenomeViews-method seqnames,BSgenomeViews-method
> ###   start,BSgenomeViews-method end,BSgenomeViews-method
> ###   width,BSgenomeViews-method strand,BSgenomeViews-method
> ###   ranges,BSgenomeViews-method elementNROWS,BSgenomeViews-method
> ###   seqinfo,BSgenomeViews-method coerce,BSgenomeViews,DNAStringSet-method
> ###   coerce,BSgenomeViews,XStringSet-method
> ###   as.character,BSgenomeViews-method as.data.frame,BSgenomeViews-method
> ###   extractROWS,BSgenomeViews-method getListElement,BSgenomeViews-method
> ###   seqtype,BSgenomeViews-method nchar,BSgenomeViews-method
> ###   unlist,BSgenomeViews-method alphabetFrequency,BSgenomeViews-method
> ###   hasOnlyBaseLetters,BSgenomeViews-method
> ###   uniqueLetters,BSgenomeViews-method
> ###   letterFrequency,BSgenomeViews-method
> ###   oligonucleotideFrequency,BSgenomeViews-method
> ###   nucleotideFrequencyAt,BSgenomeViews-method
> ###   consensusMatrix,BSgenomeViews-method
> ###   consensusString,BSgenomeViews-method show,BSgenomeViews-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> library(BSgenome.Mmusculus.UCSC.mm10)
> genome <- BSgenome.Mmusculus.UCSC.mm10
> library(TxDb.Mmusculus.UCSC.mm10.knownGene)
Loading required package: GenomicFeatures
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")'.

> txdb <- TxDb.Mmusculus.UCSC.mm10.knownGene
> ex <- exons(txdb, columns=c("exon_id", "tx_name", "gene_id"))
> v <- Views(genome, ex)
> v
BSgenomeViews object with 256721 views and 3 metadata columns:
                 seqnames             ranges strand                       dna |
                    <Rle>          <IRanges>  <Rle>            <DNAStringSet> |
       [1]           chr1 [4807893, 4807982]      + [GCACTGTCCG...CACCGCCGCG] |
       [2]           chr1 [4808455, 4808486]      + [GTTATTTTCC...GAGATACAGG] |
       [3]           chr1 [4828584, 4828649]      + [GCATGGATGG...GTCCACATGC] |
       [4]           chr1 [4830268, 4830315]      + [CCCTGTGATG...TGCCTTCTTG] |
       [5]           chr1 [4832311, 4832381]      + [GTTTGATATC...GCAGAAACCG] |
       ...            ...                ...    ...                       ... .
  [256717] chrUn_JH584304     [55512, 55701]      - [GTGTCCCTGT...TTCTTCTGGC] |
  [256718] chrUn_JH584304     [55740, 57151]      - [GTTGTACTTT...AGTACTCAAA] |
  [256719] chrUn_JH584304     [56986, 57151]      - [GTTGTACTTT...CCTGAGCAGG] |
  [256720] chrUn_JH584304     [58564, 58835]      - [CTGTGGTCCT...CAGAGAAATG] |
  [256721] chrUn_JH584304     [59592, 59689]      - [TCTCTGCTGC...GCCTTCTCAG] |
             exon_id               tx_name         gene_id
           <integer>       <CharacterList> <CharacterList>
       [1]         1 uc007afg.1,uc007afh.1           18777
       [2]         2 uc007afg.1,uc007afh.1           18777
       [3]         3 uc007afg.1,uc007afh.1           18777
       [4]         4 uc007afg.1,uc007afh.1           18777
       [5]         5 uc007afg.1,uc007afh.1           18777
       ...       ...                   ...             ...
  [256717]    256717            uc029xhi.1           66776
  [256718]    256718            uc029xho.1           66776
  [256719]    256719            uc029xhj.1           66776
  [256720]    256720 uc029xhj.1,uc029xho.1           66776
  [256721]    256721 uc029xhi.1,uc029xho.1           66776
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome
> 
> subject(v)
Mouse genome:
# organism: Mus musculus (Mouse)
# provider: UCSC
# provider version: mm10
# release date: Dec. 2011
# release name: Genome Reference Consortium GRCm38
# 66 sequences:
#   chr1                 chr2                 chr3                
#   chr4                 chr5                 chr6                
#   chr7                 chr8                 chr9                
#   chr10                chr11                chr12               
#   chr13                chr14                chr15               
#   ...                  ...                  ...                 
#   chrUn_GL456372       chrUn_GL456378       chrUn_GL456379      
#   chrUn_GL456381       chrUn_GL456382       chrUn_GL456383      
#   chrUn_GL456385       chrUn_GL456387       chrUn_GL456389      
#   chrUn_GL456390       chrUn_GL456392       chrUn_GL456393      
#   chrUn_GL456394       chrUn_GL456396       chrUn_JH584304      
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> granges(v)
GRanges object with 256721 ranges and 0 metadata columns:
                 seqnames             ranges strand
                    <Rle>          <IRanges>  <Rle>
       [1]           chr1 [4807893, 4807982]      +
       [2]           chr1 [4808455, 4808486]      +
       [3]           chr1 [4828584, 4828649]      +
       [4]           chr1 [4830268, 4830315]      +
       [5]           chr1 [4832311, 4832381]      +
       ...            ...                ...    ...
  [256717] chrUn_JH584304     [55512, 55701]      -
  [256718] chrUn_JH584304     [55740, 57151]      -
  [256719] chrUn_JH584304     [56986, 57151]      -
  [256720] chrUn_JH584304     [58564, 58835]      -
  [256721] chrUn_JH584304     [59592, 59689]      -
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome
> seqinfo(v)
Seqinfo object with 66 sequences (1 circular) from mm10 genome:
  seqnames       seqlengths isCircular genome
  chr1            195471971      FALSE   mm10
  chr2            182113224      FALSE   mm10
  chr3            160039680      FALSE   mm10
  chr4            156508116      FALSE   mm10
  chr5            151834684      FALSE   mm10
  ...                   ...        ...    ...
  chrUn_GL456392      23629      FALSE   mm10
  chrUn_GL456393      55711      FALSE   mm10
  chrUn_GL456394      24323      FALSE   mm10
  chrUn_GL456396      21240      FALSE   mm10
  chrUn_JH584304     114452      FALSE   mm10
> as(v, "DNAStringSet")
  A DNAStringSet instance of length 256721
         width seq
     [1]    90 GCACTGTCCGCCAGCCGGTGGATGTGCGGCA...TGTGCCGGCCGCCCGGAAGGCCACCGCCGCG
     [2]    32 GTTATTTTCCTTCACGGATTGGGAGATACAGG
     [3]    66 GCATGGATGGGCAGAAGCCTTTGCAGGTATC...GTCCCCACATCAAATACATCTGTCCACATGC
     [4]    48 CCCTGTGATGCCAGTCACATTAAATATGAATATGGCTATGCCTTCTTG
     [5]    71 GTTTGATATCGTTGGACTTTCACCAGATTCC...GAATCTGGAATTAAACAGGCAGCAGAAACCG
     ...   ... ...
[256717]   190 GTGTCCCTGTATAAAACTGTGCCAACTCGTT...CACTACCACAACCTCAGCGAGTTCTTCTGGC
[256718]  1412 GTTGTACTTTCCCCAGCTGGCCCTATGGCGG...TGCGGGGTTGGAGTATATGAAAGTACTCAAA
[256719]   166 GTTGTACTTTCCCCAGCTGGCCCTATGGCGG...CAGCCAGGTGGGATGGAGGCCCCTGAGCAGG
[256720]   272 CTGTGGTCCTCTAACCTGTGCCTGTGAGCCA...CAGGACCGGAGCTCCAAGCAGCAGAGAAATG
[256721]    98 TCTCTGCTGCCGGAGCAAGCTCAGCTGTCCC...TGGACAGGAAGACTCTCTCCGGCCTTCTCAG
> 
> v10 <- v[1:10]  # select the first 10 views
> subject(v10)    # same as subject(v)
Mouse genome:
# organism: Mus musculus (Mouse)
# provider: UCSC
# provider version: mm10
# release date: Dec. 2011
# release name: Genome Reference Consortium GRCm38
# 66 sequences:
#   chr1                 chr2                 chr3                
#   chr4                 chr5                 chr6                
#   chr7                 chr8                 chr9                
#   chr10                chr11                chr12               
#   chr13                chr14                chr15               
#   ...                  ...                  ...                 
#   chrUn_GL456372       chrUn_GL456378       chrUn_GL456379      
#   chrUn_GL456381       chrUn_GL456382       chrUn_GL456383      
#   chrUn_GL456385       chrUn_GL456387       chrUn_GL456389      
#   chrUn_GL456390       chrUn_GL456392       chrUn_GL456393      
#   chrUn_GL456394       chrUn_GL456396       chrUn_JH584304      
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> granges(v10)
GRanges object with 10 ranges and 0 metadata columns:
       seqnames             ranges strand
          <Rle>          <IRanges>  <Rle>
   [1]     chr1 [4807893, 4807982]      +
   [2]     chr1 [4808455, 4808486]      +
   [3]     chr1 [4828584, 4828649]      +
   [4]     chr1 [4830268, 4830315]      +
   [5]     chr1 [4832311, 4832381]      +
   [6]     chr1 [4837001, 4837074]      +
   [7]     chr1 [4839387, 4839488]      +
   [8]     chr1 [4840956, 4841132]      +
   [9]     chr1 [4840956, 4842827]      +
  [10]     chr1 [4844963, 4846735]      +
  -------
  seqinfo: 66 sequences (1 circular) from mm10 genome
> seqinfo(v10)    # same as seqinfo(v)
Seqinfo object with 66 sequences (1 circular) from mm10 genome:
  seqnames       seqlengths isCircular genome
  chr1            195471971      FALSE   mm10
  chr2            182113224      FALSE   mm10
  chr3            160039680      FALSE   mm10
  chr4            156508116      FALSE   mm10
  chr5            151834684      FALSE   mm10
  ...                   ...        ...    ...
  chrUn_GL456392      23629      FALSE   mm10
  chrUn_GL456393      55711      FALSE   mm10
  chrUn_GL456394      24323      FALSE   mm10
  chrUn_GL456396      21240      FALSE   mm10
  chrUn_JH584304     114452      FALSE   mm10
> as(v10, "DNAStringSet")
  A DNAStringSet instance of length 10
     width seq
 [1]    90 GCACTGTCCGCCAGCCGGTGGATGTGCGGCAAC...GTTGTGCCGGCCGCCCGGAAGGCCACCGCCGCG
 [2]    32 GTTATTTTCCTTCACGGATTGGGAGATACAGG
 [3]    66 GCATGGATGGGCAGAAGCCTTTGCAGGTATCAAAAGTCCCCACATCAAATACATCTGTCCACATGC
 [4]    48 CCCTGTGATGCCAGTCACATTAAATATGAATATGGCTATGCCTTCTTG
 [5]    71 GTTTGATATCGTTGGACTTTCACCAGATTCCCA...ATGAATCTGGAATTAAACAGGCAGCAGAAACCG
 [6]    74 TAAAAGCCTTGATAGATCAAGAAGTGAAGAATG...TCTAACAGGATTATTTTGGGAGGATTTTCTCAG
 [7]   102 GGAGGCGCCTTGTCTTTATACACTGCTCTCACC...TGCTGGCTTCCACTTCGGGCTTCGTTTTCACAG
 [8]   177 GGGCCGATCAACAGTGCTAATCGAGATATTTCC...TATGAAGGCATGATGCACAGCTCATGTCAGCAG
 [9]  1872 GGGCCGATCAACAGTGCTAATCGAGATATTTCC...GTTAACTGTAACGAAAAGGTGAGGTTGAAGGGT
[10]  1773 GAAATGATGGATGTCAAGCACTTCATTGATAAG...ATCAATGTGAAATAAAATTTAATTTTGGCTTTA
> alphabetFrequency(v10)
        A   C   G   T M R W S Y K V H D B N - + .
 [1,]  12  36  30  12 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [2,]   7   5   9  11 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [3,]  20  18  14  14 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [4,]  12  11   9  16 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [5,]  23  14  17  17 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [6,]  24  10  17  23 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [7,]  18  31  24  29 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [8,]  50  40  36  51 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [9,] 594 332 423 523 0 0 0 0 0 0 0 0 0 0 0 0 0 0
[10,] 582 285 289 617 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> alphabetFrequency(v10, collapse=TRUE)
   A    C    G    T    M    R    W    S    Y    K    V    H    D    B    N    - 
1342  782  868 1313    0    0    0    0    0    0    0    0    0    0    0    0 
   +    . 
   0    0 
> 
> v12 <- v[width(v) <= 12]  # select the views of 12 nucleotides or less
> head(as.data.frame(v12))
  seqnames     start       end width strand exon_id      tx_name gene_id
1     chr1  40008331  40008339     9      +    1052 uc007atr....   26921
2     chr1  44119184  44119195    12      +    1244   uc007awe.2  246229
3     chr1  58393097  58393103     7      +    1840   uc007bbq.1   66882
4     chr1  87844112  87844121    10      +    3621   uc007bxs.1   20215
5     chr1 135803282 135803285     4      +    5318   uc033flq.1   21952
6     chr1 135841901 135841911    11      +    5339 uc007ctu....   21956
           dna
1    GGAGAAGTG
2 CGCAAATGGCAG
3      GGCGGGG
4   CAAAAGAAAG
5         TGAG
6  GGAACAGGAAG
> trinucleotideFrequency(v12, simplify.as="collapsed")
AAA AAC AAG AAT ACA ACC ACG ACT AGA AGC AGG AGT ATA ATC ATG ATT CAA CAC CAG CAT 
139  91 176  74  90  55  29 144 139  79 177  79  96  57 168 103  98  50 129  59 
CCA CCC CCG CCT CGA CGC CGG CGT CTA CTC CTG CTT GAA GAC GAG GAT GCA GCC GCG GCT 
 89  88  20 104  12   9  35   7 127  86 140  92 139  86 177 138  70  71  13 101 
GGA GGC GGG GGT GTA GTC GTG GTT TAA TAC TAG TAT TCA TCC TCG TCT TGA TGC TGG TGT 
211  74 306 107  98  48  62  67  75 125  81 125  76  98  15 115 112  67 201  48 
TTA TTC TTG TTT 
 92  88  80  91 
> 
> ## BSgenomeViews objects are list-like objects. That is, the
> ## BSgenomeViews class derives from List and typical list/List
> ## operations (e.g. [[, elementNROWS(), unlist(), elementType(),
> ## etc...) work on these objects:
> is(v12, "List")  # TRUE
[1] TRUE
> v12[[2]]
  12-letter "DNAString" instance
seq: CGCAAATGGCAG
> head(elementNROWS(v12))  # elementNROWS(v) is the same as width(v)
[1]  9 12  7 10  4 11
> unlist(v12) 
  8065-letter "DNAString" instance
seq: GGAGAAGTGCGCAAATGGCAGGGCGGGGCAAAAGAA...AAACAACAAACAATTGTCCCTGGAGAGATGGTGCCA
> elementType(v12)
[1] "DNAString"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO