[R-sig-genetics] Available R packages to QC/summarize large SNP datasets?

[GRIGNOLA, FERNANDO E [AG/1000]]

Hi,

I looking for some guidance regarding available packages to do QC (i.e.
parent-offspring inheritance checks) and to summarize large SNP datasets
(i.e. 50K) for pedigreed populations (frequencies, linkage calculations,
etc).

I know of some packages that check for HW equilibrium, get frequencies
as part of the data preparation for genome-wide association analyses for
example. However, I was wondering if somebody can point me to 1 or 2
packages that mostly focus on data quality and summary statistics for
large SNPs of data.

Thanks in advance for your assistance,

 

Fernando

 

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