GenABEL is not part of Bioconductor.  The authors and their email addresses
are noted in the DESCRIPTION
file, visible through help(package="GenABEL").  Your best bet is to contact
them.

Additional details seem necessary to help you -- what exactly did you use to
read the file you describe, and
what is your sessionInfo()?

On Mon, May 18, 2009 at 8:06 PM, Ping-Hsun Hsieh <hsiehp@ohsu.edu> wrote:

>
>
> Dear R/BioC experts,
>
>
>
> I am interested in the R package “GenABEL”  and would like to test it on my
> dataset, but not successful.
>
> My toy dataset, 9 samples x 1000 SNPs, were successfully converted into
> gwaa.data class, however, its coding does not look right to me.
>
>
>
> Here is part of the genotype file.
>
> name    chr          pos         strand   MDSNP_02         MDSNP_04
> MDSNP_06         MDSNP_07         MDSNP_08         MDSNP_10
>  MDSNP_11         MDSNP_12         MDSNP_15
>
> SNP_A-2131660                1              1145994                +
>       CT           CT           TT           TT           TT           TT
>         TT           TT           CT
>
> SNP_A-1967418                1              2224111                +
>       GG         GG         GG         GG         AG          AG          GG
>         GG         GG
>
> SNP_A-1969580                1              2319424                +
>       GG         GG         GG         GG         GG         GG         GG
>       GG         GG
>
> SNP_A-4263484                1              2543484                +
>       TT           CT           CT           CC           CC           TT
>         TT           TT           CT
>
> SNP_A-1978185                1              2926730                -
>        CC           CC           CC           CC           CC           CC
>         CC           CC           CC
>
> SNP_A-4264431                1              2941694                -
>        CT           CC           CC           CC           CC           CC
>         CT           CT           CC
>
> SNP_A-1980898                1              3084986                -
>        GG         GG         GG         GG         GG         GG         CG
>          CG          GG
>
> SNP_A-1983139                1              3155127                +
>       AC          AA          AA          AA          AA          AA
>  AA          AA          AA
>
>
>
> The coding of the first sample, for first 9 SNPs only.
>
> >as.character(toydf@gtdata)[1,1:9]
>
> SNP_A-2131660                SNP_A-1967418               SNP_A-1969580
>            SNP_A-4263484                SNP_A-1978185
>
>        "T/C"                             "G/G"
>        "1/1"                                     "T/T"
>               "1/1"
>
> SNP_A-4264431                SNP_A-1980898                SNP_A-1983139
>            SNP_A-4265735
>
>        "C/T"                              "G/G"
>       "A/C"                                    "C/T"
>
>
>
> The coding of the third SNP, “SNP_A-1969580”, for all 9 samples.
>
> > as.character(toydf@gtdata)[1:9,3]
>
> MDSNP_02         MDSNP_04        MDSNP_06         MDSNP_07        MDSNP_08
>
>  "1/1"                           "1/1"               "1/1"
>           "1/1"                "1/1"
>
> MDSNP_10         MDSNP_11         MDSNP_12        MDSNP_15
>
> "1/1"                           "1/1"                "1/1"
>           "1/1"
>
>
>
> As you can see, for example, SNP_A-1969580 are GG across 9 samples. Why
> does the coding of this SNP show “1/1”, rather than “G/G”?
>
>
>
> The other question I have, also related to the above question, is if it is
> required to have DNA bases in the genotype file.
>
> Could I use AA,AB, and BB as coding scheme, rather than the exact bases in
> GenABEL? Will it give troubles/errors?
>
>
>
> Thanks for your answer/response in advance!
>
>
>
> Best Regards,
>
> Mike
>
>
>
>
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>
>
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>



-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265

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