Entering edit mode
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.timeexport.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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