PLINK? (also contains a ~"plugin" for to 'R': http://pngu.mgh.harvard.edu/~purcell/plink/rfunc.shtml

I managed to found a web portal to compute basic statistics on SNP data, such allele frequencies and association with a trait.

Here is the link: http://bioinfo.iconcologia.net/snpstats/start.htm

Regards

Have you tried SCANDB http://scan.bsd.uchicago.edu/ ?

Apart from plink and arlequin, I suggest GenePop. It can be used as a command-line tool or through a web interface. It also has some APIs inside biopython.

Take a look at the R/Bioconductor snpMatrix package, from David Clayton. It was successfully applied in large GWAS, e.g.

The Wellcome Trust Case Control Consortium. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447: 661-678.

GenAbel also provides very interesting options to summarize and quality check SNP data.

having only hundreds of markers on hundreds of samples, I guess PLINK is far too powerful. although it may do what you need, it may also be too complex as it is intended to deal with many thousands of markers on thousands of samples. you may want to consider using other very well established tools such as Arlequin (an integrated software for population genetics data analysis), which you may find here: http://cmpg.unibe.ch/software/arlequin35/

I will add GLU to the list.

GLU: GENOTYPE LIBRARY AND UTILITIES Whole-genome association studies are generating unprecedented amounts of genotype data, frequently billions of genotypes per study, and require new and scalable computational approaches to address the storage, management, quality control, and genetic analysis. GLU is a framework and a software package that was designed around a set of novel conceptual approaches. GLU addresses the need for general and powerful tools that can scale to effectively handle trillions of genotypes.

http://code.google.com/p/glu-genetics/

Since the OP requested an R package for HWE, Allelefreq and Association. I would recommend the package called SNPAssoc

You can download the package from CRAN

http://cran.r-project.org/web/packages/#available-packages-S

SNPassoc: an R package to perform whole genome association studies Juan R. González, Lluís Armengol, Xavier Solé, Elisabet Guinó, Josep M. Mercader, Xavier Estivill and Víctor Moreno[?] Reference: Sole, Guino, Valls, Iniesta, Moreno (2006), "SNPStats: a web tool for the analysis of association studies", Bioinformatics, 22(15):1928-1929.