Gviz import bed file for AnnotationTrack
0
0
Entering edit mode
@florianhahnenovartiscom-3784
Last seen 5.5 years ago
Switzerland
Should be fixed now in version 1.4.4 Florian On 6/27/13 2:48 AM, "Christopher DeBoever" <cdeboeve at="" ucsd.edu=""> wrote: >Hi all, I'm trying to import a bed file into Gviz and getting an error >(see >below). Has anyone encountered this error? > >Thanks, > >Chris DeBoever > >Frazer Laboratory >Bioinformatics and Systems Biology >University of California San Diego > >> library(Gviz) >Loading required package: grid >> atrack = AnnotationTrack("test3.bed",genome="hg19") >Error in .local(range, ...) : object 'cmpa' not found >> sessionInfo() >R version 3.0.1 (2013-05-16) >Platform: x86_64-apple-darwin10.8.0 (64-bit) > >locale: >[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > >attached base packages: >[1] grid stats graphics grDevices utils datasets methods >[8] base > >other attached packages: >[1] Gviz_1.4.2 > >loaded via a namespace (and not attached): > [1] AnnotationDbi_1.22.6 Biobase_2.20.0 BiocGenerics_0.6.0 > [4] biomaRt_2.16.0 Biostrings_2.28.0 biovizBase_1.8.1 > [7] bitops_1.0-5 BSgenome_1.28.0 cluster_1.14.4 >[10] colorspace_1.2-2 DBI_0.2-7 dichromat_2.0-0 >[13] GenomicFeatures_1.12.2 GenomicRanges_1.12.4 Hmisc_3.10-1.1 >[16] IRanges_1.18.1 labeling_0.2 lattice_0.20-15 >[19] munsell_0.4 parallel_3.0.1 plyr_1.8 >[22] RColorBrewer_1.0-5 RCurl_1.95-4.1 Rsamtools_1.12.3 >[25] RSQLite_0.11.4 rtracklayer_1.20.2 scales_0.2.3 >[28] stats4_3.0.1 stringr_0.6.2 tools_3.0.1 >[31] XML_3.95-0.2 zlibbioc_1.6.0 >> > >Example lines from bed file: > >chr22 23229959 23230008 f1 0 >chr9 2653832 2654480 f2 0 > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor
Gviz Gviz • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 891 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6