[R] Character SNP data to binary MAF data

Hadassa Brunschwig
Thu, 29 Jan 2009 08:08:47 -0000

Hi

An example is as follows. Consider the character 3x6 matrix:

a A a T A t
G g t T T t
A a C C c c

For each row I would like to identify the most frequent letter and
assign a 1 to it and 0
to the less frequent character. That is, in row 1 the most frequent
letter is A (I do not differentiate between capital and non-capital
letters), in row 2 T and in row 3 C. After the binary conversion
the resulting matrix would look like that:

1 1 1 0 1 0
0 0 1 1 1 1
0 0 1 1 1 1

Any suggestions on how to do that (and I am sure I am not the first
one to try this).

Thanks
Hadassa


On Thu, Jan 29, 2009 at 1:50 AM, Jorge Ivan Velez
<jorgeivanvelez at gmail.com> wrote:
>
> Hi Hadassa,
> Do you have a sample of your data and the output you want? It might be
> useful for us in order to provide any help to you.
> Regards,
>
> Jorge
>
>
> On Wed, Jan 28, 2009 at 8:36 AM, Hadassa Brunschwig
> <hadassa.brunschwig at mail.huji.ac.il> wrote:
>>
>> Hi
>>
>> I am sure there is a function out there already but I couldn't find
it.
>> I have SNP data, that is, a matrix which contains in each row two
>> characters (they are different in each row) and I would like to
>> convert this matrix to a binary one according to the minor allele
>> frequency. For non-geneticists: I want to have a binary matrix
>> for which in each row the 0 stands for the less frequent character
>> and 1 for the more frequent character.
>>
>> Thanks for any suggestions.
>> Hadassa
>>
>> --
>> Hadassa Brunschwig
>> PhD Student
>> Department of Statistics
>> The Hebrew University of Jerusalem
>> http://www.stat.huji.ac.il
>>
>> ______________________________________________
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>> and provide commented, minimal, self-contained, reproducible code.
>
>



--
Hadassa Brunschwig
PhD Student
Department of Statistics
The Hebrew University of Jerusalem