[BioC] Error in GenomicRanges trying to append two GRangesLists
Elizabeth Purdom
epurdom at stat.berkeley.edu
Fri Sep 10 21:43:23 CEST 2010
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
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