[BioC] IRanges: RangedData rbind error
Jonathan Cairns
Jonathan.Cairns at cancer.org.uk
Wed Nov 24 15:09:06 CET 2010
Hi all,
I seem to be getting an error message on trying to use rbind() on two relatively innocuous-looking RangedData objects - see below. I was wondering if anyone else has had the same problem. This works fine on simpler objects, so my guess would be that these particular objects are malformed in some way but I'm not sure how I would check that.
I can get around this by manually coercing each RangedData object to a data.frame, but that approach seems suboptimal to me.
Thanks,
Jonathan
--------
> a
RangedData with 3032 rows and 0 value columns across 25 spaces
space ranges |
<character> <IRanges> |
1 chr1 [1274369, 1274619] |
2 chr1 [1310219, 1310569] |
3 chr1 [1907419, 1907769] |
4 chr1 [1983269, 1983469] |
5 chr1 [2355219, 2355319] |
6 chr1 [2431369, 2432219] |
7 chr1 [2446219, 2446619] |
8 chr1 [3441819, 3442169] |
9 chr1 [3657769, 3657919] |
... ... ... ...
3024 chrX [106724271, 106724371] |
3025 chrX [106983671, 106983771] |
3026 chrX [108586171, 108586271] |
3027 chrX [108781571, 108781671] |
3028 chrX [110424871, 110425571] |
3029 chrX [152256221, 152256371] |
3030 chrX [152619071, 152619221] |
3031 chrX [152661471, 152662221] |
3032 chrX [152662571, 152662671] |
> names(a) ##n.b. no ranges present for space "chrM"
[1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"
[10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5"
[19] "chr6" "chr7" "chr8" "chr9" "chrM" "chrX" "chrY"
> b
RangedData with 6486 rows and 0 value columns across 23 spaces
space ranges |
<character> <IRanges> |
1 chr1 [1274159, 1274912] |
2 chr1 [1309807, 1310770] |
3 chr1 [1532507, 1532754] |
4 chr1 [1907180, 1907982] |
5 chr1 [1983127, 1983848] |
6 chr1 [2354988, 2355437] |
7 chr1 [2431031, 2432299] |
8 chr1 [2433599, 2433985] |
9 chr1 [2446015, 2446750] |
... ... ... ...
6478 chrX [152618904, 152619429] |
6479 chrX [152660747, 152661246] |
6480 chrX [152661264, 152662298] |
6481 chrX [152662420, 152662899] |
6482 chrX [152664180, 152664467] |
6483 chrX [152665288, 152665502] |
6484 chrX [152758426, 152758742] |
6485 chrX [153591715, 153591957] |
6486 chrX [153849434, 153849749] |
> names(b) ## (chrY, chrM not present in this object)
[1] "chr1" "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"
[10] "chr18" "chr19" "chr2" "chr20" "chr21" "chr22" "chr3" "chr4" "chr5"
[19] "chr6" "chr7" "chr8" "chr9" "chrX"
> rbind(a,b)
Error in .Method(..., deparse.level = deparse.level) :
column names for arg 23 do not match those of first arg
> traceback()
17: stop("column names for arg ", i, " do not match those of first arg")
16: .Method(..., deparse.level = deparse.level)
15: eval(expr, envir, enclos)
14: eval(.dotsCall, env)
13: eval(.dotsCall, env)
12: standardGeneric("rbind")
11: function (..., deparse.level = 1)
standardGeneric("rbind")(<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">, <S4 object of class "DataFrame">,
<S4 object of class "DataFrame">)
10: do.call(rbind, unname(x))
9: .compress.list(lapply(unlistData, as, elementTypeData))
8: newCompressedList("CompressedSplitDataFrameList", listData)
7: SplitDataFrameList(do.call(Map, c(list(safe.rbind), dfs)))
6: .Method(..., deparse.level = deparse.level)
5: eval(expr, envir, enclos)
4: eval(.dotsCall, env)
3: eval(.dotsCall, env)
2: standardGeneric("rbind")
1: rbind(a, b)
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
[3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.utf8
[7] LC_PAPER=en_GB.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rtracklayer_1.10.0 RCurl_1.4-3 bitops_1.0-4.1 IRanges_1.8.2
loaded via a namespace (and not attached):
[1] Biobase_2.10.0 Biostrings_2.18.0 BSgenome_1.18.0
[4] GenomicRanges_1.2.1 tools_2.12.0 XML_3.2-0
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