Sorry… I forgot to attach the session info… here it is:

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] snpStats_1.12.0 Matrix_1.1-0    survival_2.37-4

loaded via a namespace (and not attached):
[1] BiocGenerics_0.8.0 grid_3.0.2         lattice_0.20-24    parallel_3.0.2

[5] tools_3.0.2



2014/1/23 francesca casalino <francy.casalino@gmail.com>

>  Hi all,
> I am trying to read a file called "chr1.gen" that contains imputation
> posterior probabilities (3 values per SNP) and SNP names in the second
> column, and I am trying to use the snpStats function "read.impute", but
> when I try to read the whole file:
>
> x=read.impute("chr1.gen"))
>
>  I get the following error message:
>
> Error in read.impute("chr.gen") :
> input field exceeds buffer length
>
> However the data seems to load when I set a limit for the number of SNPs:
>
>  x=read.impute("chr1.gen",nsnp=200)
>
>  Does anyone know what this error means? Is it expecting maybe a subset of
> the file, or is this an R issue? I could not find any examples of this on
> the web, so if you have encountered this error before please let me know.
>
> Thank you
>
> -fra
>
>

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