This function calculates the fixation index Fst for each SNP, together with its weight in the overall estimate (as used by the Internation HapMap Consortium).
Classes of objects created by snp.lhs.tests and snp.rhs.tests. The class "GlmTestsScore" extends the class "GlmTests" and is invoked by setting the argument score=TRUE when calling testing functions in order to save the scores and their variances (and covariances)
A class defining a list "rules" for imputation of SNPs. Rules are estimated population haplotype probabilities for a target SNP and one or more predictor SNPs
These are classes to hold the objects created by single.snp.tests and provide methods for extracting key elements. The class "SingleSnpTestsScore" extends class "SingleSnpTests" to include the score and score variance statistics in order to provide methods for pooling results from several studies or parts of a study
These functions convert snpMatrix objects to snpStats objects. convert.snpMatrix converts a single object, while convert.snpMatrix.dir converts all stored elements in a specified directory. They really only change the class names since most of the classes in snpStats are backwards-compatible with snpMatrix. The exception is the ImputationRules class; imputation.rules objects will need to be regenerated.
Determine which imputation rules are broken by removal of some SNPs from a study. This function is needed because, when if it emerges that genotyping of some SNPs is not reliable, necessitating their removal from study, we would also wish to remove any SNPs imputed on the basis of these unreliable SNPs.
providing 
.