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 2 3 0
control 2 2 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 1 0 2 1
case 0 1 1 2
case 1 2 2 0
control 0 1 0 1
control 1 2 1 2
control 0 0 0 0
case 1 0 2 2
case 0 1 2 1
control 1 0 0 1
--
Thanks,
Jim.
[[alternative HTML version deleted]]
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 2 3 0
> control 2 2 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 1 0 2 1
> case 0 1 1 2
> case 1 2 2 0
> control 0 1 0 1
> control 1 2 1 2
> control 0 0 0 0
> case 1 0 2 2
> case 0 1 2 1
> control 1 0 0 1
>
>
> --
> Thanks,
> Jim.
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
[[alternative HTML version deleted]]