[Bioc-devel] Modification of seqnames in GRanges

[Liu,Bin]

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