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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