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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2014-06-13 15:04:19 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20140613150419-v49mxnlg42rnuks5
Tags: 1.16.3-1
* New upstream version
* New (Build-)Depends: r-bioc-genomeinfodb
* cme fix dpkg-control
* add autopkgtest

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man/Seqinfo-class.Rd
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\alias{isCircular<-,Seqinfo-method}
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\alias{genome,Seqinfo-method}
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\alias{genome<-,Seqinfo-method}
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\alias{seqnameStyle,Seqinfo-method}
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\alias{seqnameStyle<-,Seqinfo-method}
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\alias{[,Seqinfo-method}
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\alias{coerce,Seqinfo,GRanges-method}
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\alias{coerce,Seqinfo,GenomicRanges-method}
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      Get/set the genome identifier or assembly name for each sequence
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      in \code{x}.
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    }
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    \item{}{
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      \code{seqnameStyle(x)}:
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      Get/set the seqname style for \code{x}.
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      Note that this information is not stored in \code{x} but inferred
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      by looking up \code{seqnames(x)} against a seqname style database
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      stored in the seqnames.db metadata package (required).
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      The getter can return more than 1 seqname style (with a warning)
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      in case the style cannot be determined unambiguously.
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    }
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  }
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}
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seqlengths(x)
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isCircular(x)
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genome(x)
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seqnameStyle(x)  # UCSC
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seqnameStyle(x) <- "NCBI"
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seqlevels(x)
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seqnameStyle(x)  # NCBI (ambiguous)
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seqnameStyle(x) <- "UCSC"
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seqlevels(x)
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x[c("chrY", "chr3", "chr1")]  # subset by names
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