useful tools for parsing HapMap-structured genotype/ped files are found in
the snpMatrix package.

On Tue, Jan 6, 2009 at 6:44 AM, Basu, Analabha <BasuA@humgen.ucsf.edu>wrote:

> Dear All,
>
> I am trying to read genetic data for unrelated individuals with
> readGenes() function.
>
> The first two lines of my data (for the first 2 genotypes and the usual
> "family", "pid", "father", "mother", "sex", "affection" columns are as
> follows:
>
>
>
> 2001 2001 0 0 1 1 2 2 1 2
>
> 2003 2003 0 0 1 1 1 2 1 1
>
>
>
> I am getting the following error message :
>
>
>
> *       Mx_C_BC<-readGenes.hapmap.ped(filename="Mx_C_hapmap.ped")
>
>
>
> Error in readGenes.ped(filename = filename, columns = c("family", "pid",
> :
>
>  Unable to determine file dimensions for ped file `Mx_C_hapmap.ped'.
>
>
>
> Or if I use
>
> > Mx_C_BC <- readGenes(gfile="Mx_C_hapmap.ped", gformat = "hapmap")
>
> Error in readGenes.ped(filename = filename, columns = c("family", "pid",
> :
>
>  Unable to determine file dimensions for ped file `Mx_C_hapmap.ped'.
>
>
>
>
>
> I was following instruction from
>
> www.bioconductor.org/packages/2.3/bioc/vignettes/GeneticsBase/inst/doc/H
> OWTO-LoadGenotypes.pdf<http://www.bioconductor.org/packages/2.3/bioc/vignettes/GeneticsBase/inst/doc/HOWTO-LoadGenotypes.pdf>
> <http://www.bioconductor.org/packages/2.3/bioc/vignettes/GeneticsBase/in
> st/doc/HOWTO-LoadGenotypes.pdf<http://www.bioconductor.org/packages/2.3/bioc/vignettes/GeneticsBase/inst/doc/HOWTO-LoadGenotypes.pdf>
> >
>
>
>
> I am also copying the session info if that helps
>
>
>
> >
>
> > sessionInfo()
>
> R version 2.6.1 (2007-11-26)
>
> i386-pc-mingw32
>
>
>
> locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
>
>
>
> other attached packages:
>
>  [1] fbat_1.2.0           MASS_7.2-42          GeneticsDesign_1.4.0
>
>  [4] gmodels_2.14.1       GeneticsBase_1.2.0   haplo.stats_1.3.8
>
>  [7] mvtnorm_0.9-0        gplots_2.6.0         gtools_2.4.0
>
> [10] combinat_0.0-6       xtable_1.5-2         gdata_2.4.2
>
>
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.6.1
>
>
>
>
>
> Thanks in advance,
>
> --analabha
>
>
>
>
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>
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