[Bioc-devel] Modification of seqnames in GRanges

[Cook, Malcolm]

Thanks for the pointer.

I think those are only in 2.9.... to be released any day now....

Cheers,

~Malcolm


> -----Original Message-----
> From: Valerie Obenchain [mailto:vobencha at fhcrc.org]
> Sent: Friday, October 28, 2011 6:13 PM
> To: Liu,Bin
> Cc: Cook, Malcolm; 'bioc-devel at r-project.org'
> Subject: Re: [Bioc-devel] Modification of seqnames in GRanges
> 
> Liu and Bin,
> 
> For more general use you might be interested in.
> 
> ?keepSeqlevels
> ?renameSeqlevels
> 
> in the GenomicRanges package.
> 
> Valerie
> 
> 
> 
> On 10/28/2011 02:26 PM, Liu,Bin wrote:
> > Thanks a lot! It works!
> >
> > Bin
> >
> >
> > -----Original Message-----
> > From: Cook, Malcolm [mailto:MEC at stowers.org]
> > Sent: Friday, October 28, 2011 1:57 PM
> > To: Liu,Bin; 'bioc-devel at r-project.org'
> > Subject: RE: Modification of seqnames in GRanges
> >
> > Hi Bin,
> >
> > I think I have you covered....
> >
> >
> > UCSC2FlybaseGRanges<- function (GRanges) {
> > ### Rename the chromosomes in<GRanges>  from UCSC conventions
> ('chr1',
> > ### etc) to comport with Flybase conventions ('1', etc) by stripping
> > ### leading 'chr' and translating 'M' as 'dmel_mitochondrion_genome'.
> >    ## old way:?
> >    ## levels(seqnames(BSgenome))<-
> factor(Rle(sub('chr','',levels(seqnames(BSgenome)))))
> >    ##
> levels(seqnames(BSgenome))[levels(seqnames(BSgenome))=="M"]<-
> "dmel_mitochondrion_genome"
> >    seqlevels(GRanges)<- sub('chr','',seqlevels(GRanges))
> >    seqlevels(GRanges)<-
> sub('M','dmel_mitochondrion_genome',seqlevels(GRanges))
> >    GRanges
> > }
> >
> > Flybase2UCSC_ID<-function(ID)
> gsub('^(.*)$','chr\\1',sub('dmel_mitochondrion_genome','M',ID))
> >
> > Flybase2UCSCGRanges<- function (GRanges) {
> > ### converse of UCSC2FlybaseGRanges()
> >    seqlevels(GRanges)<-
> sub('dmel_mitochondrion_genome','M',seqlevels(GRanges))
> >    seqlevels(GRanges)<- gsub('^(.*)$','chr\\1',seqlevels(GRanges))
> >    GRanges
> > }
> >
> > Regards,
> >
> > ~Malcolm
> >
> >
> >> -----Original Message-----
> >> From: bioc-devel-bounces at r-project.org [mailto:bioc-devel-bounces at r-
> >> project.org] On Behalf Of Liu,Bin
> >> Sent: Friday, October 28, 2011 11:56 AM
> >> To: bioc-devel at r-project.org
> >> Subject: [Bioc-devel] Modification of seqnames in GRanges
> >>
> >> Hi,
> >>      I have a question about how to modify the seqnames in below. I would
> like
> >> to remove chr in the seqnames.
> >> For example: "chr2L" ->  "2L". I tried the following code and got an error:
> >>
> >>> seqnames(gr1)<- sub("chr", "", seqnames(gr1))
> >> Error in `seqnames<-`(`*tmp*`, value =<S4 object of class "Rle">) :
> >>    levels of supplied 'seqnames' must be identical to 'seqlevels(x)'
> >>
> >>
> >>    With the following checking, it seems chrM is not in seqnames but is in
> the
> >> levels.
> >>> levels(seqnames(gr1))
> >>   [1] "chr2L"     "chr2LHet"  "chr2R"     "chr2RHet"  "chr3L"     "chr3LHet"
> >>   [7] "chr3R"     "chr3RHet"  "chr4"      "chrU"      "chrUextra" "chrX"
> >> [13] "chrXHet"   "chrYHet"   "chrM"
> >>
> >>> unique(seqnames(gr1))
> >>   [1] chr2L     chr2LHet  chr2R     chr2RHet  chr3L     chr3LHet  chr3R
> >>   [8] chr3RHet  chr4      chrU      chrUextra chrX      chrXHet   chrYHet
> >> 15 Levels: chr2L chr2LHet chr2R chr2RHet chr3L chr3LHet chr3R chr3RHet ...
> >> chrM
> >>
> >>     Any way to solve the problem?   Thanks for the help.
> >>
> >> Bin Liu
> >>
> >>
> >>> gr1
> >> GRanges with 48498 ranges and 0 elementMetadata values:
> >>            seqnames           ranges strand
> >>               <Rle>         <IRanges>   <Rle>
> >>        [1]    chr2L   [ 8117,  8192]      +
> >>        [2]    chr2L   [11345, 11409]      +
> >>        [3]    chr2L   [11519, 11778]      +
> >>        [4]    chr2L   [12222, 12285]      +
> >>        [5]    chr2L   [12929, 13519]      +
> >>        [6]    chr2L   [13626, 13682]      +
> >>        [7]    chr2L   [14875, 14932]      +
> >>        [8]    chr2L   [15712, 17052]      +
> >>        [9]    chr2L   [17213, 18025]      +
> >>        ...      ...              ...    ...
> >>    [48490]  chrYHet [191815, 191893]      +
> >>    [48491]  chrYHet [192066, 206119]      +
> >>    [48492]  chrYHet [229343, 232315]      +
> >>    [48493]  chrYHet [232496, 232758]      +
> >>    [48494]  chrYHet [233403, 233455]      +
> >>    [48495]  chrYHet [233595, 271120]      +
> >>    [48496]  chrYHet [280371, 291285]      +
> >>    [48497]  chrYHet [305380, 305531]      +
> >>    [48498]  chrYHet [306016, 306486]      +
> >>    ---
> >>    seqlengths:
> >>         chr2L  chr2LHet     chr2R  chr2RHet ...   chrXHet   chrYHet      chrM
> >>      23011544    368872  21146708   3288761 ...    204112    347038     19517
> >>
> >> _______________________________________________
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