[BioC] rtracklayer Rle to bigWig (export.bw ?)

[Arnaud Amzallag]

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