Question: rtracklayer Rle to bigWig (export.bw ?)
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gravatar for Arnaud Amzallag
8.4 years ago by
Arnaud Amzallag100 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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