[R] Hardy Weinberg

[David Winsemius]

On Jun 22, 2011, at 11:57 PM, Jim Silverton wrote:

> I am generating 1,000 replicates of 10,000 of these 2 x 3 tables but R
> cannot seem to save it.

What does that mean? Error messages?

> Its over 1 Gig. Any ideas on how I can store this
> large amount of data? Should I use a list or a matrix?

How about an array?

--  
David.
>
> Jim
>
> On Wed, Jun 22, 2011 at 10:21 PM, Mike Miller <mbmiller+l at gmail.com>  
> wrote:
>
>> On Thu, 23 Jun 2011, David Duffy wrote:
>>
>> I am interested in simulating 10,000 2 x 3 tables for SNPs data  
>> with the
>>>> Hardy Weinberg formulation. Is there a quick way to do this? I am  
>>>> assuming
>>>> that the minor allelle frequency is uniform in (0.05, 0.25).
>>>>
>>>
>>> rmultinom() with HWE expectations
>>>
>>
>>
>> I'm also unsure of what the 2x3 table is (what are the rows?), and  
>> David
>> gave you a good answer for how to make tabular data, but I just  
>> thought I'd
>> add some info for those who may be interested...
>>
>> If you want to make genotype data in the form of minor allele  
>> counts under
>> HW, you can use rbinom() with size=2 and prob=MAF.
>>
>> Suppose variable "n" is the number of subjects for whom data is to be
>> generated, "maf" is a vector of minor allele frequencies, and "m"  
>> is the
>> length of maf (i.e., the number of markers to be generated.  Then  
>> this will
>> produce a data matrix (subjects by markers):
>>
>> maf <- c( .1, .2, .5 )
>>> n <- 7
>>> m <- length( maf )
>>> t( matrix( rbinom( n*m, 2, maf ), m, n ) )
>>>
>>    [,1] [,2] [,3]
>> [1,]    0    0    2
>> [2,]    0    1    1
>> [3,]    1    0    2
>> [4,]    0    2    1
>> [5,]    1    1    1
>> [6,]    0    1    2
>> [7,]    0    0    1
>>
>> Of course, when data are produced that way, the markers are in  
>> linkage
>> equilibrium (an unfortunate term meaning that the genotypes for  
>> pairs of
>> markers are not associated).
>>
>> Mike
>>
>> --
>> Michael B. Miller, Ph.D.
>> Minnesota Center for Twin and Family Research
>> Department of Psychology
>> University of Minnesota
>>
>
>
>
> -- 
> Thanks,
> Jim.
>
> 	[[alternative HTML version deleted]]
>
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David Winsemius, MD
West Hartford, CT