Hi,

This issue was fixed about a month ago in devel. A simple work-around is
this:

export.bw(covplus, "test275p.bigWig", genome="hg18")

Btw, you should probably update to R 2.13 and use the latest stable version
of the package (which is still broken though).

Thanks,
Michael

On Wed, Jun 29, 2011 at 3:05 PM, Arnaud Amzallag
<arnaud.amzallag@gmail.com>wrote:

> Hello to all,
>
> I am trying to make a bigWig for loading in UCSC from a SimpleRleList. I
> cannot find an exemple so I just tried, but I get an error (Error in
> is.null(genome) : 'genome' is missing).
>
> If someone could send me the correct code for this (if this is implemented
> at all) that would be nice. I copy here the code I tried to run, if it helps
> explaining my problem.
>
> Thank you in advance,
>
> Arnaud Amzallag
> Massachusetts General Hospital / Harvard Medical School
>
>
> >library(rtracklayer)
> >system.time(export.bw(covplus, "test275p.bigWig",
> seqlengths=hg18lengths[1:24]))
> Error in is.null(genome) : 'genome' is missing
> Timing stopped at: 98.631 5.122 103.771
>
> A glimpse at my variables :
>
> > hg18lengths[1:24]
>     chr1      chr2      chr3      chr4      chr5      chr6      chr7
>  chr8
> 247249719 242951149 199501827 191273063 180857866 170899992 158821424
> 146274826
>     chr9     chr10     chr11     chr12     chr13     chr14     chr15
> chr16
> 140273252 135374737 134452384 132349534 114142980 106368585 100338915
>  88827254
>    chr17     chr18     chr19     chr20     chr21     chr22      chrX
>  chrY
>  78774742  76117153  63811651  62435964  46944323  49691432 154913754
>  57772954
>
>
> > covplus
> SimpleRleList of length 24
> $chr1
> 'numeric' Rle of length 247249719 with 4300893 runs
>  Lengths:    68     2     4     1     1 ...     4    19    39    33 50134
>  Values :     0   0.2  0.31  0.51  0.59 ...  0.36   0.2     0  0.12     0
>
> $chr2
> 'numeric' Rle of length 242951149 with 3652830 runs
>  Lengths:      3     39      8      6     30 ...     30      4     29
> 200080
>  Values :      0   0.03      0   0.01   0.14 ...    0.1      0   0.14
>  0
>
> $chr3
> 'numeric' Rle of length 199501827 with 2965480 runs
>  Lengths: 35873    35   884    13    16 ...     5     6     2     4 55004
>  Values :     0  0.99     0     1  1.06 ...  0.19  0.13  0.09  0.04     0
>
> $chr4
> 'numeric' Rle of length 191273063 with 2607751 runs
>  Lengths:     1     1     3     1     1 ...     1    38     4    36 10013
>  Values :  0.03   0.1  0.11  0.55  0.64 ...   0.2  0.11     0  0.19     0
>
> $chr5
> 'numeric' Rle of length 180857866 with 3111948 runs
>  Lengths: 63442     6     4     4     1 ...    40    25     9    17 20044
>  Values :     0  0.06  0.12  0.13  0.26 ...     0  0.24  0.44   0.2     0
>
> ...
> <19 more elements>
>
> > sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] rtracklayer_1.10.6    RCurl_1.4-3           bitops_1.0-4.1
>  [4] multicore_0.1-5       aaRnaSeq_1.02         DESeq_1.2.1
>  [7] locfit_1.5-6          lattice_0.19-13       akima_0.5-4
> [10] Biobase_2.10.0        GenomicFeatures_1.2.1 Rsamtools_1.2.1
> [13] Biostrings_2.18.0     GenomicRanges_1.2.1   IRanges_1.8.9
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.28.0      AnnotationDbi_1.12.0 biomaRt_2.6.0
>  [4] BSgenome_1.18.1      DBI_0.2-5            genefilter_1.32.0
>  [7] geneplotter_1.28.0   grid_2.12.0          RColorBrewer_1.0-2
> [10] RSQLite_0.9-3        splines_2.12.0       survival_2.35-8
> [13] tools_2.12.0         XML_3.2-0            xtable_1.5-6
>
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