Question: RCircos 2D track plot for a small region of genome
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5.9 years ago by
Guest User12k
Guest User12k wrote:
Hi I???ve been working with the R package RCircos for a short while. I???d like to make Circos 2D track plot localized to a small region of genome (say 700kb-800kb on chr1). Does anyone know how this can be done? -Mark -- output of sessionInfo(): R version 3.0.2 (2013-09-25) 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] splines grid parallel stats graphics grDevices utils datasets methods base other attached packages: [1] rtracklayer_1.22.0 Rsamtools_1.14.2 RCircos_1.1.2 BSgenome.Hsapiens.UCSC.hg18_1.3.19 [5] BSgenome_1.30.0 Biostrings_2.30.1 faraway_1.0.5 plyr_1.8 [9] pscl_1.04.4 vcd_1.3-1 gam_1.09 coda_0.16-1 [13] mvtnorm_0.9-9996 MASS_7.3-29 Hmisc_3.13-0 Formula_1.1-1 [17] survival_2.37-4 lattice_0.20-24 cluster_1.14.4 GenomicRanges_1.14.4 [21] XVector_0.2.0 IRanges_1.20.6 BiocGenerics_0.8.0 Matrix_1.1-1.1 loaded via a namespace (and not attached): [1] bitops_1.0-6 colorspace_1.2-4 RCurl_1.95-4.1 stats4_3.0.2 tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 -- Sent via the guest posting facility at bioconductor.org.
bsgenome • 1.0k views
ADD COMMENTlink modified 4.7 years ago by Hu, Ying NIH/NCI [E]50 • written 5.9 years ago by Guest User12k
Answer: RCircos 2D track plot for a small region of genome
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gravatar for Dan Tenenbaum
5.9 years ago by
Dan Tenenbaum8.2k
United States
Dan Tenenbaum8.2k wrote:
Hi Mark, ----- Original Message ----- > From: "Mark Carty [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, mac449 at cornell.edu > Sent: Thursday, January 2, 2014 1:41:02 PM > Subject: Re: [BioC] RCircos 2D track plot for a small region of genome > > > Hi > > I???ve been working with the R package RCircos for a short while. > I???d like to make Circos 2D track plot localized to a small region > of genome (say 700kb-800kb on chr1). Does anyone know how this can > be done? > > -Mark RCircos is not a Bioconductor package so I don't know how much help we can provide. You might try contacting the maintainer: packageDescription("RCircos")$Maintainer A similar package which is a BioC package is OmicCircos: http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html Dan > > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > 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] splines grid parallel stats graphics grDevices > utils datasets methods base > > other attached packages: > [1] rtracklayer_1.22.0 Rsamtools_1.14.2 > RCircos_1.1.2 > BSgenome.Hsapiens.UCSC.hg18_1.3.19 > [5] BSgenome_1.30.0 Biostrings_2.30.1 > faraway_1.0.5 plyr_1.8 > [9] pscl_1.04.4 vcd_1.3-1 > gam_1.09 > coda_0.16-1 > [13] mvtnorm_0.9-9996 MASS_7.3-29 > Hmisc_3.13-0 > Formula_1.1-1 > [17] survival_2.37-4 lattice_0.20-24 > cluster_1.14.4 > GenomicRanges_1.14.4 > [21] XVector_0.2.0 IRanges_1.20.6 > BiocGenerics_0.8.0 > Matrix_1.1-1.1 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 colorspace_1.2-4 RCurl_1.95-4.1 stats4_3.0.2 > tools_3.0.2 XML_3.95-0.2 zlibbioc_1.8.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 >
ADD COMMENTlink written 5.9 years ago by Dan Tenenbaum8.2k
Answer: RCircos 2D track plot for a small region of genome
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gravatar for Hu, Ying NIH/NCI [E]
4.7 years ago by
United States
Hu, Ying NIH/NCI [E]50 wrote:

By the updated version, http://master.bioconductor.org/packages/3.1/bioc/html/OmicCircos.html, you can plot any genome regions by using the updated segAnglePo function.

ADD COMMENTlink written 4.7 years ago by Hu, Ying NIH/NCI [E]50
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