You could follow the advice given when loading the library (see the code you posted for details) and use the enhanced genetics packages to cross-validate the results (ideally you should get the same answer).
The results not weird though. Your working with SNPs and having a homozygote with a frequency of zero isn't that unlikely, it depends on the minor allele frequency (MAF). In this instance its the controls you appear to be concerned about, and for this locus the MAF of the minor allele is 0.0145, so in a sample of 173 individuals you would expect to see 0.0363 individuals with the recessive genotype (basic Mendelian genetics of 173 * 0.0145^2). Thus at best you might expect to see one person in a sample of that size, but its not surprising that you've not seen any. You may also find the following references of interest... Guangyong Zou, Allan Donner The Merits of Testing Hardy-Weinberg Equilibrium in the Analysis of Unmatched Case-Control Data: A Cautionary Note Annals of Human Genetics Volume 70, Issue 6, Pages 923-933 (basically advocates the use of a robust test for association such as the trend test over the two-stage design of testing for HWeqm and then testing for association). There is follow up discussion of the article in Yik Y. Teo, Andrew E. Fry, Taane G. Clark, E. S. Tai, Mark Seielstad On the Usage of HWE for Identifying Genotyping Errors Annals of Human Genetics Volume 71 Issue 5 , Pages 701 - 703 ...and a rejoinder from Zou and Donner... Guangyong Zou, Allan Donner The Reply of Zou & Donner to Teo's Commentary on their Manuscript (p 704-704) Annals of Human Genetics Volume 71 Issue 5 , Pages 701 - 703 Neil Sun, Ying [BSD] - HGD wrote: > > ============ >> library( "genetics" ) > NOTE: THIS PACKAGE IS NOW OBSOLETE. > The R-Genetics project has developed an set of enhanced genetics > packages to replace 'genetics'. Please visit the project homepage > at http://rgenetics.org for informtion. > -- View this message in context: http://www.nabble.com/help-needed-for-HWE.exact-in-library-%22genetics%22-tp19100974p19105112.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.