Sorry about this. You need to have installed the BSgenome package for hg18 for this to work. I just made a change to devel so that it will fall back to the UCSC genome browser if the BSgenome package is not found. Michael On Sat, Jul 2, 2011 at 5:09 PM, Arnaud Amzallag wrote: > Thank you michael, > > but I did not have much success with this command on R 2.13. Should I > install the R-devel version, or do you think there is a solution on the > "release" ? > > Best, > > Arnaud > > > system.time(export.bw(covplus, "test275p.bigWig", genome="hg18")) > Error in seqlengths(seqinfo(x)) : > error in evaluating the argument 'x' in selecting a method for function > 'seqlengths': Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "seqinfo", for signature > "NULL" > Timing stopped at: 113.49 9.684 123.196 > > > sessionInfo() > R version 2.13.0 (2011-04-13) > 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_1.12.4 RCurl_1.6-6 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.20.1 BSgenome_1.20.0 GenomicRanges_1.4.6 > [4] IRanges_1.10.4 tools_2.13.0 XML_3.4-0 > > > > On Jul 1, 2011, at 3:14 AM, Michael Lawrence wrote: > > 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > [[alternative HTML version deleted]]