[BioC] Correlation analysis

[Sean Davis]

On Mon, Nov 7, 2011 at 6:00 PM, Minh Bui <buiduyminh at gmail.com> wrote:
> HI Sean,
>
> Thank you for the quick answer.
>
> By correlation analysis, I mean I want to see if those HIV sequences fall
> into the genes or not. If so, what kind of test I should do?

Hi, Minh.

Either source I sent should deal with that question easily.  Overlaps
of two sets of genomic regions are what both deal with very well.

Sean


> I will check those two sources out.
>
> Thanks,
>
>
>
>
> On Mon, Nov 7, 2011 at 5:56 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>> Hi, Minh.
>>
>> By "correlation analysis", you mean that you want to find the gene
>> closest to each HIV site?  If so, take a look at the GenomicRanges
>> package.
>>
>> If you are more of a web server point-and-click person, take a look at
>> using galaxy:
>>
>> http://main.g2.bx.psu.edu/
>>
>> Sean
>>
>>
>> On Mon, Nov 7, 2011 at 5:52 PM, Minh Bui <buiduyminh at gmail.com> wrote:
>> > Hi everyone,
>> >
>> > I am new to Bioconductor and R. I did search through the list for my
>> > problem but i can't find it. I am sorry if this question has been asked.
>> >
>> > I would like to perform a correlation analysis between a hiv data and
>> gene
>> > expression.
>> >
>> > Basically, i have a file that contains: hiv_name, start_position,
>> > end_position, chromosome. I would like to see if these data has anything
>> to
>> > do with the location of our genes (I also have another file contains
>> > gene_name, start_position, end_position, chromosome).
>> >
>> > What functions that allow me to do this?
>> >
>> > Hopefully someone can guide me to the right direction.
>> >
>> >
>> > Thank you very much,
>> >
>> > --
>> >
>> >
>> ------------------------------------------------------------------------------------
>> > Minh Bui
>> > Bioinformatic Research, MicroBiome Analysis Center
>> > George Mason University, Prince William Campus
>> > 10900 University Boulevard, MSN 4D4
>> > Manassas, Virginia  20110
>> > http://mbac.gmu.edu
>> >
>> ------------------------------------------------------------------------------------
>> >
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>> >
>>
>
>
>
> --
>
> ------------------------------------------------------------------------------------
> Minh Bui
> Bioinformatic Research, MicroBiome Analysis Center
> George Mason University, Prince William Campus
> 10900 University Boulevard, MSN 4D4
> Manassas, Virginia  20110
> http://mbac.gmu.edu
> ------------------------------------------------------------------------------------
>
>        [[alternative HTML version deleted]]
>
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