[BioC] Bioconductor / plotting SNPs, runs of homozygosity
Vincent Carey
stvjc at channing.harvard.edu
Mon Jul 12 21:58:41 CEST 2010
I am sorry to say that this query does not seem very clear to me.
There are plenty of facilities for visualizing
genomic data in Bioconductor, and general graphical facilities of R
might be suitable for what you are seeking.
The data have a block structure over genomic coordinates and if you
can get plink to emit that data in
bed format, for example, the rtracklayer package could import it for
further numerical manipulation. Clearly if you can make
bed format you can do visualization in the browser by importing a
custom track. But the details of what you
want to show from the ROH data need to be clarified before further
suggestions can be made.
On Mon, Jul 12, 2010 at 3:47 PM, Min-Han Tan <minhan.tan at gmail.com> wrote:
> Good afternoon all,
>
> Sorry to trouble you all. I am quite new to plotting high throughput SNPs /
> chromosome locations, and am trying to visualize some SNP data generated by
> Plink. (Illumina 330K)
>
> I am wondering which package would be most useful (and ideally Illumina
> friendly). I looked at geneplotter, and SNPchip, but am not sure whether
> there was a quick way to start. For e.g. it looks like SNPchip is more
> Affymetrix based. Essentially, the data is runs of homozygosity. I have
> start and end coordinates (with corresponding SNPs) for each of these runs
> (example data below, for one pool of data)
>
> (CON refers to the consensus region - i.e. the region common to all, which
> in this case is actually 0 KB, but this isn't always the case)
> (UNION refers to the entire region spanned by the overlapping segments of
> homozygosity).
>
> Any advice would be appreciated. Thanks!
>
> Min-Han
>
>
> POOL FID IID PHE CHR SNP1 SNP2 BP1 BP2 KB
> NSNP NSIM GRP
> S34481 0 X1 1 12 rs4883195 rs11053499 8924893
> 9939332 1014.44 211 1 1
> S34481 0 X2 2 12 rs10771151 rs7297150 8920868
> 10087355 1166.49 271 1 1
> S34481 0 X3 2 12 rs7308209 rs12310310 8920732
> 10375281 1454.55 350 1 1
> S34481 0 X4 2 12 rs2707209 rs4883195 6775525
> 8924893 2149.37 351 3 1*
> S34481 0 X5 2 12 rs917589 rs7968375 3412660
> 12393268 8980.61 2188 0 2*
> S34481 0 X6 1 12 rs4310684 rs11053781 8034750
> 10428536 2393.79 481 0 3*
> S34481 0 X7 1 12 rs2241025 rs619563 8136239
> 9982949 1846.71 330 0 4*
> S34481 0 X8 2 12 rs11043394 rs6488666 8153839
> 14284369 6130.53 1491 0 5*
> S34481 0 X9 1 12 rs1894814 rs2537760 8880044
> 10375636 1495.59 374 0 6*
> S34481 CON 9 5:04 12 rs4883195 rs4883195 8924893
> 8924893 0 1 NA NA
> S34481 UNION 9 5:04 12 rs917589 rs6488666 3412660
> 14284369 10871.7 2757 NA NA
>
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>
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