Hi Jonathan,

Could you please send me a simple reproducible example? I think I've fixed
this, but I can't really be sure.

Thanks,
Michael

On Wed, Nov 24, 2010 at 6:09 AM, Jonathan Cairns <
Jonathan.Cairns@cancer.org.uk> wrote:

> 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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