Hi Liz:

The problem is you are not specifying the id argument as a character
string.  The documentation describes the value of this argument to be the
column name of the id variable.

e.g.:

ped.1 <- Pedigree( tp , subject = "id" , ascendant = c( "sire" , "dam" ) )

will work.

Thanks!!

Dave H
On Jul 21, 2013 1:37 PM, "Dan Tenenbaum" <dtenenba@fhcrc.org> wrote:

> CC'ing GeneticsPed maintainer.
>
> On Sun, Jul 21, 2013 at 12:56 PM, Liz Hare <doggene@earthlink.net> wrote:
> > Hello,
> >
> > I'm trying to make a Pedigree object in GeneticsPed.
> >
> > Data in test2.csv:
> >
> > id,sire,dam
> > 1,,
> > 2,,
> > 3,,
> > 4,,
> > 5,1,2
> > 6,3,4
> > 7,5,6
> > 8,5,6
> >
> > R session:
> >
> >> tp <- read.csv("test2.csv", header=TRUE)
> >> ped.1 <- Pedigree(ped, subject = tp$id, ascendant = c("sire", "dam"))
> > Error in .subset2(x, i, exact = exact) :
> >   recursive indexing failed at level 2
> >
> >> sessionInfo()
> > R version 2.15.1 (2012-06-22)
> > Platform: x86_64-pc-linux-gnu (64-bit)
> >
> > locale:
> >  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >  [7] LC_PAPER=C                 LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] GeneticsPed_1.18.0 genetics_1.3.8     mvtnorm_0.9-9995   MASS_7.3-23
> > [5] gtools_3.0.0       combinat_0.0-8     gdata_2.13.2
> >
> > loaded via a namespace (and not attached):
> > [1] compiler_2.15.1 tools_2.15.1
> >
> > ==============================================
> >
> > I also had this problem with R 3.0.1 and GeneticsPed 1.22.0 in 64-bit
> > Windows. I've tried it with other pedigrees and it doesn't work there,
> > either.
> >
> > I have read the package documentation and searched the Bioconductor site,
> > and not found anything that appears to apply to this situation.
> >
> > Thanks for any ideas!
> >
> > Liz
> >
> > --
> > Liz Hare PhD
> > Dog Genetics LLC
> > doggene@earthlink.net
> > http://www.doggenetics.com
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>

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