Hi Jim,
Here is one way:
# data
x - structure(list(category = structure(c(1L, 1L, 1L, 2L, 2L, 2L,
1L, 1L, 2L), .Label = c(case, control), class = factor),
SNP1 = c(1L, 0L, 1L, 0L, 1L, 0L, 1L, 0L, 1L), SNP2 = c(0L,
1L, 2L, 1L, 2L, 0L, 0L, 1L, 0L), SNP3 = c(2L, 1L, 2L, 0L,
1L, 0L, 2L, 2L, 0L)), .Names = c(category, SNP1, SNP2,
SNP3), class = data.frame, row.names = c(NA, -9L))
# transforming SNPs to factors with levels 0, 1, 2
x[, -1] - lapply(x[, -1], function(x) factor(x, levels = 0:2))
# processing
res - lapply(colnames(x)[-1], function(name) table(x[, 1], x[, name]))
names(res) - colnames(x)[-1]
res
HTH,
Jorge
On Wed, Jul 27, 2011 at 12:23 AM, Jim Silverton wrote:
Hello,
I have indicators for the present of absent of a snps in columns and the
categorey (case control column). I would like to extract ONLY the tables
and
the indices (SNPS) that give me 2 x 3 tables. Some gives 2x 2 tables when
one of the allelle is missing. The data look like the matrix snpmat below:
so the first snp should give me the following table: (aa=0, Aa=1 and AA=2)
aa Aa AA
case 23 0
control 22 0
So I should not use this one or if I am using it, then I need to see 0 0
in
to AA column which I don't see when I use the table command in R.
snpmat
category SNP1 SNP2 SNP3 SNPN
case 102 1
case 011 2
case 122 0
control 0 1 01
control 1 21 2
control 0 00 0
case1 02 2
case0 121
control 1 00 1
--
Thanks,
Jim.
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