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 <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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