Hi Skirmantas,

I've cc'd this to the Bioc mailing list; hope you don't mind. IGB cannot
handle bigWig yet (we are working on it), so bedGraph is your best option.
The error below is a bug, but your code would eventually fail, because I'm
guessing there is no "genome" entry (e.g., hg19) in the metadata on that
object.  Without that, or the genome argument or seqlengths argument, BigWig
export is not possible (it requires the chromosome lengths). In this case,
the seqlengths are probably just the elementLengths of your SimpleRleList
(as long as you gave them to the coverage method).

Michael

On Thu, Apr 28, 2011 at 8:09 AM, Skirmantas Kriaucionis <
skirmantas.kriaucionis@ludwig.ox.ac.uk> wrote:

> Dear Michael,
>
>
>
> After recent upgrade I am having a problem to export SimpleRleList object
> which is generated by “coverage” to wig. I get
>
>
>
> Error in FUN(X[i], ...) :
>
>   The span must be uniform for Wiggle export. Consider bedGraph or bigWig
> as alternatives.
>
>
>
> BigWig could probably do (I have to see how IGB handles it), but I get an
> error as well:
>
>
>
> Error in is.null(genome) : 'genome' is missing
>
>
>
> Do you have any advice?
>
> My data file looks like this:
>
>
>
> SimpleRleList of length 21
>
> $chr1
>
> 'integer' Rle of length 197195432 with 1276791 runs
>
>   Lengths: 3000568      67      37     336 ...    2354     440    6008
> 226
>
>   Values :       0       1       2       3 ...       0       1
> 0       1
>
>
>
> $chr2
>
> 'integer' Rle of length 181748087 with 1518743 runs
>
>   Lengths: 3001054     440    4523     440 ...       1      79
> 4       2
>
>   Values :       0       1       0       1 ...      24      22      21
> 20
>
>
>
> $chr3
>
> 'integer' Rle of length 159599783 with 947316 runs
>
>   Lengths: 3001016      24     416      24 ...     440    2135     440
> 504
>
>   Values :       0       1       2       1 ...       1       0
> 1       0
>
>
>
> $chr4
>
> 'integer' Rle of length 155630120 with 1361168 runs
>
>   Lengths: 3002410     440    3481     270 ...     110      72      13
> 16
>
>   Values :       0       1       0       1 ...       5       4
> 3       2
>
>
>
> $chr5
>
> 'integer' Rle of length 152537259 with 1458847 runs
>
>   Lengths: 3002270      24      51     365 ...      50     464     440
> 62
>
>   Values :       0       1       2       3 ...       1       0
> 1       0
>
>
>
> ...
>
> <16 more elements>
>
>
>
> Best wishes,
>
> Skirmantas K.
>
>
>
> Skirmantas Kriaucionis, phD
>
> Ludwig Institute for Cancer Research LTD
>
> Nuffield Department of Clinical Medicine
>
> University of Oxford
>
> Old Road Campus Research Building
>
> Roosevelt Drive
>
> Oxford OX3 7DQ
>
> UK
>
>
>
> Tel +44 (0)1865 617536
>
> Fax +44 (0)1865 617542
>
>
>

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