[BioC] Bioconductor / plotting SNPs, runs of homozygosity

[Vincent Carey]

GenomeGraphs is another relevant package.  Look at the vignette.  The
problem is not completely straightforward to solve but you can compute
the ratios and locations using R alone, or if you find additional
facilities for rendering aspects of genomic context in GenomeGraphs
useful, then go for it and perhaps you can write/contribute some
utilities for nice renderings of this sort of data.  This particular
problem of graphing MIGHT have been solved outside of bioconductor, so
going over the packages in the CRAN task views "genetics" view and
checking the plink related list may be in order.

On Mon, Jul 12, 2010 at 4:19 PM, Min-Han Tan <minhan.tan at gmail.com> wrote:
> I apologize.
>
> To clarify - I have runs of homozygosity data that vary in terms of
> cases/control ratios. (in the example below, it would be 5 cases: 4 controls
> for this particular pool).
>
> Ideally, I would like to be able to plot for each chromosome a graph - y
> axis being the case/control ratio; x axis = distance along chromosome. Each
> ROH segment would be marked out along the chromosome, based on the input
> data format.
>
> Sorry if this question seems extremely straightforward, and thanks for the
> pointer to rtracklayer.
>
> Min-Han
>
>
>
>
> On Mon, Jul 12, 2010 at 3:58 PM, Vincent Carey <stvjc at channing.harvard.edu>
> wrote:
>>
>> 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
>> >
>> >        [[alternative HTML version deleted]]
>> >
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