Ok I get it now,
If your data is as shown i.e. sorted, then can you just create a dummy
variable:
rep(1:10,n) where n is the number of groups and then use by or tapply?
So in your example:
by(df[,4],rep(1:10,2),mean)

cheers,
Achilleas

On Thu, May 12, 2011 at 12:38 PM, Fabrice Tourre <fabrice.ciup@gmail.com>wrote:

> Thanks for your reply. But it cannot be for my purpose. In fact, there
> are two snps in the example, rs9971029 and rs9971030.
>
> I expect fellow output with the fellow data:
>
> 0.35 0.45 0.35 0.80 0.50 1.00 2.30 0.80 0.90 0.90
>
> You can run this example to get above value
>
> -----------------------------R code------------------------------------
> df<-structure(list(seqnames = structure(c(1L, 1L, 1L, 1L, 1L, 1L,
> 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), .Label =
> "chr10", class = "factor"),
>    snp.id = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
>    1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("rs9971029",
>    "rs9971030"), class = "factor"), position = c(71916552L,
>    71916553L, 71916554L, 71916555L, 71916556L, 71916557L, 71916558L,
>    71916559L, 71916560L, 71916561L, 71916726L, 71916727L, 71916728L,
>    71916729L, 71916730L, 71916731L, 71916732L, 71916733L, 71916734L,
>    71916735L), score = c(0.1, 0.4, 0.3, 0.9, 1, 2, 4, 0.8, 0.9,
>    0.8, 0.6, 0.5, 0.4, 0.7, 0, 0, 0.6, 0.8, 0.9, 1)), .Names =
> c("seqnames",
> "snp.id", "position", "score"), class = "data.frame", row.names = c(NA,
> -20L))
>
> a<-df[1:10,]
> b<-df[11:20,]
> cbind(a,b)->c
> (c[,4]+c[,8])/2
> ----------------------------------------------------------------
>
> The data is :
>
> chr10   rs9971029   71916552    0.1
> chr10   rs9971029   71916553    0.4
> chr10   rs9971029   71916554    0.3
> chr10   rs9971029   71916555    0.9
> chr10   rs9971029   71916556    1
> chr10   rs9971029   71916557    2
> chr10   rs9971029   71916558    4
> chr10   rs9971029   71916559    0.8
> chr10   rs9971029   71916560    0.9
> chr10   rs9971029   71916561    0.8
> chr10   rs9971030   71916726    0.6
> chr10   rs9971030   71916727    0.5
> chr10   rs9971030   71916728    0.4
> chr10   rs9971030   71916729    0.7
> chr10   rs9971030   71916730    0
> chr10   rs9971030   71916731    0
> chr10   rs9971030   71916732    0.6
> chr10   rs9971030   71916733    0.8
> chr10   rs9971030   71916734    0.9
> chr10   rs9971030   71916735    1
>
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