Hi folks,
i'm trying to compare a few different GRanges objects (such as mutations made by me, SNPs from SNPlocs.Hsapiens.dbSNP.20101109 and transcripts from GenomicFeatures), and since the dbSNP data package uses 'ch1' as opposed to 'chr1', I need to coerce the seqnames so that they can be matched. 
Here's the error:

> snps <- getSNPlocs("ch17", as.GRanges=TRUE)
> seqnames(snps) <- rep('chr17', length(snps))
Error in validObject(.Object) : 
  invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed character vector with no NAs

According to the man page this should be doable:
?`seqnames,GRanges-method`
   ‘seqnames(x)’, ‘seqnames(x) <- value’: Gets or sets the sequence names.
          ‘value’ can be an Rle object, character vector, or factor.

# Try using an Rle:
> seqnames(snps) <- Rle(rep('chr17', length(snps)))
Error in validObject(.Object) : 
  invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed character vector with no NAs


Reproducible code in a fresh R session:
library(SNPlocs.Hsapiens.dbSNP.20101109)
snps <- getSNPlocs("ch17", as.GRanges=TRUE)
seqnames(snps) <- rep('chr17', length(snps))
Error in validObject(.Object) : 
  invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed character vector with no NAs

snps
GRanges with 641905 ranges and 2 elementMetadata values
         seqnames               ranges strand   |   RefSNP_id alleles_as_ambig
            <Rle>            <IRanges>  <Rle>   | <character>      <character>
     [1]     ch17         [ 293,  293]      *   |     9747578                R
     [2]     ch17         [ 828,  828]      *   |    62053745                Y
     [3]     ch17         [ 834,  834]      *   |     9747082                R
     [4]     ch17         [1389, 1389]      *   |    62053747                R
     [5]     ch17         [1397, 1397]      *   |    34845611                Y
     [6]     ch17         [1665, 1665]      *   |    34151105                Y
     [7]     ch17         [1869, 1869]      *   |    62053748                W
     [8]     ch17         [1880, 1880]      *   |    77383171                Y
     [9]     ch17         [1897, 1897]      *   |    75157665                R
     ...      ...                  ...    ... ...         ...              ...
[641897]     ch17 [81180274, 81180274]      *   |    74430365                R
[641898]     ch17 [81189713, 81189713]      *   |    74334266                Y
[641899]     ch17 [81189731, 81189731]      *   |    75151244                W
[641900]     ch17 [81190324, 81190324]      *   |    76196913                S
[641901]     ch17 [81190344, 81190344]      *   |    78502756                R
[641902]     ch17 [81190367, 81190367]      *   |     2850176                Y
[641903]     ch17 [81190378, 81190378]      *   |    71264801                R
[641904]     ch17 [81190400, 81190400]      *   |    74838487                R
[641905]     ch17 [81193098, 81193098]      *   |    77334326                R

seqlengths
  ch1  ch2  ch3  ch4  ch5  ch6  ch7  ch8 ... ch19 ch20 ch21 ch22  chX  chY chMT
   NA   NA   NA   NA   NA   NA   NA   NA ...   NA   NA   NA   NA   NA   NA   NA

> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/C/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SNPlocs.Hsapiens.dbSNP.20101109_0.99.2
[2] GenomicRanges_1.2.3                   
[3] IRanges_1.8.8                         

loaded via a namespace (and not attached):
[1] tools_2.12.1




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