Is there an easily implementable analysis (R based) for copy number, ROH, mosaicism, and ploidy in R using Illumina 850K SNP array data?

Question

[Jng]

I already use karyostudio and genome studio but am curious if there are some R based packages can offer some better ways to visualize the data. Are there R-based packages that could be used for internal database formation i.e. curation of variants observed?