[BioC] Error in GenomicRanges trying to append two GRangesLists

[Elizabeth Purdom]

  Hello,
I am trying to append together two GRangesLists. I thought that either 
c() or append would allow me to do this, but I'm getting an error. My 
two GRangesLists have the same metadata column names. With both, I'm 
getting some kind of error about rownames that I don't understand and I 
just don't have any ideas about trying to track this down. My system 
information is below (R 2.11.1, GenomicRanges_1.0.9).
Thanks for any help,
Elizabeth

#my two GRangesList
 > disjointElementsCds
GRangesList of length 44
$100132288
GRanges with 6 ranges and 1 elementMetadata value
         seqnames           ranges strand | disjEx_id
<Rle> <IRanges> <Rle> | <integer>
[1] chr21_random [103280, 104416]      * |         1
[2] chr21_random [104417, 104518]      * |         2
[3] chr21_random [105133, 105363]      * |         3
[4] chr21_random [162407, 162463]      * |         4
[5] chr21_random [162464, 162465]      * |         5
[6] chr21_random [164601, 164670]      * |         6

...
<43 more elements>


seqlengths
           chr1   chr1_random         chr10  chr10_random         chr11 
...   chr9_random          chrM          chrX   chrX_random          chrY
      247249719       1663265     135374737        113275     134452384 
...       1146434         16571     154913754       1719168      57772954

 > disjointElementsNonCds
GRangesList of length 7
$152687
GRanges with 6 ranges and 1 elementMetadata value
     seqnames           ranges strand | disjEx_id
<Rle> <IRanges> <Rle> | <integer>
[1]     chr4 [ 43227,  43385]      * |         1
[2]     chr4 [ 49323,  49449]      * |         2
[3]     chr4 [ 49951,  50046]      * |         3
[4]     chr4 [ 57732,  58380]      * |         4
[5]     chr4 [184870, 185000]      * |         5
[6]     chr4 [185421, 186092]      * |         6

$26751
GRanges with 8 ranges and 1 elementMetadata value
     seqnames           ranges strand | disjEx_id
<Rle> <IRanges> <Rle> | <integer>
[1]     chr2 [208155, 209001]      * |         1
[2]     chr2 [214864, 214920]      * |         2
[3]     chr2 [219966, 220044]      * |         3
[4]     chr2 [221023, 221191]      * |         4
[5]     chr2 [223101, 223229]      * |         5
[6]     chr2 [224160, 224272]      * |         6
[7]     chr2 [237538, 237602]      * |         7
[8]     chr2 [239731, 239852]      * |         8

$403340
GRanges with 1 range and 1 elementMetadata value
         seqnames           ranges strand | disjEx_id
<Rle> <IRanges> <Rle> | <integer>
[1] chr17_random [116623, 119732]      * |         1

...
<4 more elements>


seqlengths
           chr1   chr1_random         chr10  chr10_random         chr11 
...   chr9_random          chrM          chrX   chrX_random          chrY
      247249719       1663265     135374737        113275     134452384 
...       1146434         16571     154913754       1719168      57772954

#my attempt to join them together
 > 
disjointElements<-append(disjointElementsCds,values=disjointElementsNonCds)
Error in `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771",  :
   invalid rownames length
 > disjointElements<-c(disjointElementsCds,values=disjointElementsNonCds)
Error in `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771",  :
   invalid rownames length
 > traceback()
9: stop("invalid rownames length")
8: `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771",
    "114821", "123887", "133957", "140850", "153478", "23192", "245938",
    "255403", "283768", "283897", "3081", "3166", "335", "347688",
    "3662", "375690", "375791", "3803", "3810", "389257", "404785",
    "440073", "440153", "441308", "51078", "55344", "56900", "56940",
    "5987", "642273", "643836", "6942", "7179", "727800", "81623",
    "83482", "83755", "8694", "9097", "92259", "9501", "152687",
    "26751", "403340", "644128", "645520", "64946", "653635"))
7: `rownames<-`(`*tmp*`, value = c("100132288", "10752", "10771",
    "114821", "123887", "133957", "140850", "153478", "23192", "245938",
    "255403", "283768", "283897", "3081", "3166", "335", "347688",
    "3662", "375690", "375791", "3803", "3810", "389257", "404785",
    "440073", "440153", "441308", "51078", "55344", "56900", "56940",
    "5987", "642273", "643836", "6942", "7179", "727800", "81623",
    "83482", "83755", "8694", "9097", "92259", "9501", "152687",
    "26751", "403340", "644128", "645520", "64946", "653635"))
6: .local(x, ...)
5: elementMetadata(x)
4: elementMetadata(x)
3: .c.Sequence(x, ...)
2: c(disjointElementsCds, values = disjointElementsNonCds)
1: c(disjointElementsCds, values = disjointElementsNonCds)

 > sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0

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

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

other attached packages:
[1] graph_1.26.0           projectManager_1.0     XML_3.1-1              
GenomicFeatures_1.0.10 GenomicRanges_1.0.9    IRanges_1.6.16

loaded via a namespace (and not attached):
[1] Biobase_2.8.0     biomaRt_2.4.0     Biostrings_2.16.9 
BSgenome_1.16.5   DBI_0.2-5         RCurl_1.4-2       RSQLite_0.9-2     
rtracklayer_1.8.1
[9] tools_2.11.1