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="" in="" st="" 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 [[alternative HTML version deleted]]

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/d oc/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="" geneticsbas="" e="" 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 > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]