## snpStats: Overview

This package extends the `snpMatrix` package, allowing uncertainty in genotype assignments, for example as consequence of imputation. It provides most of the functionality of `snpMatrix`, although a few functions differ somewhat from their predecessors. It also provides several new functions. Classes have had to be renamed but are mostly compatible with those in `snpMatrix`, and functions are included to convert these to their `snpStats` equivalents. However, the imputation rules objects in `snpMatrix` are not compatible with those now used and must be regenerated. For more details, see the "differences" vignette. Further development of the `snpMatrix` project by this developer will take place entirely within `snpStats`.

## Vignettes

Differences between the `snpMatrix` and `snpStats` packages:
  Equivalent classes and differences in behaviour
Example of genome-wide association testing:
  Introduction to snpStats for analysis of GWA studies
Data input in snpStats:
  Reading genotype data from various input file formats
Imputation and meta-analysis:
  Imputed SNP analyses and meta-analysis with snpStats
LD vignette:
  Measures of linkage disequilibrium
PCA vignette:
  Principal components analysis with snpStats
TDT vignette:
  Use of snpStats in family--based association studies
Fst vignette:
  Explanation of Fst calculations available in the package