[Bioc-devel] Modification of seqnames in GRanges

[Valerie Obenchain]

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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