[BioC] RCircos 2D track plot for a small region of genome

[Dan Tenenbaum]

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
> 
> --
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> 
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