[BioC] SNPassoc package data upload

[Valerie Obenchain]

Hi Magdalena,

SNPassoc is not a Bioconductor package. You could try posting your 
question to R-help at http://www.r-project.org/mail.html.

A couple of Bioconductor packages that may fit your need are snpStats, 
FunciSNP and GWAStools.

Valerie


On 02/25/2013 07:24 AM, Magdalena Wozniak wrote:
> Hi,
> I am trying to upload SNP data to SNPassoc package for basic HWE check and
> analysis of association between snp and a trait. In my file the genotypes
> are coded 0, 1, 2. I have problem in uploading it to SNPassoc package as
> the setupSNP function does not seem to accept the file without sep=""
> option. I would be very grateful for your help.
> I paste below my code.
>
>> SNPs <- read.delim("H:/genetics_data.txt")
>
>> SNPs[1:10,270:275]
>
>     phenotype snp4912075_c snp9426794_c snp6673711_c snp11506_g snp12065621_g
>
> 1          2            0            0            0          2             0
>
> 2          1            0            0            0          0             0
>
> 3          1            1            0            1          0             0
>
> 4          1            2            0            1          0             2
>
> 5          1            1            0            1          0             1
>
> 6          1            1            0            1          0             1
>
> 7          1            0            0            0          0             1
>
> 8          1            1            0            1          0             0
>
> 9          1            1            0            1          0             0
>
> 10         1            1            0            1          1             0
>
>> myData<-setupSNP(data=SNPs, colSNPs=271:534)
>
> Error in FUN(X[[1L]], ...) :
>
>    choose the correct character separator to divide alleles
>
>
>
> Thank you very much.
>
> Kind regards,
>
> Magdalena
>
>
>> sessionInfo()R version 2.15.2 (2012-10-26)
> Platform: i386-w64-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] SNPassoc_1.8-5    survival_2.37-2   haplo.stats_1.6.3
> genetics_1.3.8    mvtnorm_0.9-9994
> [6] MASS_7.3-23       gtools_2.7.0      gdata_2.12.0      combinat_0.0-8
>
> loaded via a namespace (and not attached):
> [1] tools_2.15.2
>
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>
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