I am generating 1,000 replicates of 10,000 of these 2 x 3 tables but R
cannot seem to save it. Its over 1 Gig. Any ideas on how I can store this
large amount of data? Should I use a list or a matrix?
Jim
On Wed, Jun 22, 2011 at 10:21 PM, Mike Miller <mbmille...@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.
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