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 > [[alternative HTML version deleted]]