[BioC] Are there tools of LD/recombination rate measurement in R/bioconductor

[Mao Jianfeng]

Dear bioconductor-listers,

I would like to hear your suggestions/recommendations on if there are
tools of LD/recombination rate measurement in R/bioconductor,
especially tools for whole-genome-level population genetic data, not
just for a small set of markers.

There are tools for this analysis outside R/bioconductor, like LDhat.
Months ago, I was pointed to snpMatrix2 packages. But, I have not find
a right way for me to implement snpMatrix2 in my study. So, I hope to
get your helps/directions.

Best regards,

Jian-Feng,