[Bioc-devel] Modification of seqnames in GRanges

-----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