Hierarchical Clustering of SNP Data
Clusters SNPs hierachically.
The SNP data matrix of size
The agglomeration method to be used. This should be
(an unambiguous abbreviation of) one of
The SNPs are clustered using
which performs a hierarchical cluster analysis using a set of dissimilarities
nvar objects being clustered. There are 3 possible scenarios.
d = NULL,
x is used to compute the dissimilarity matrix.
The dissimilarity measure between two SNPs is
1 - LD (Linkage
LD is defined as the square of the Pearson
correlation coefficient. If
SNP_index = NULL, all
nvar SNPs will
be clustered; otherwise only the SNPs with indices specified by
will be considered.
If the user wishes to use a different dissimilarity measure,
to be provided.
d must be either a square matrix of size
nvar x nvar, or an object of class
SNP_index will be ignored.
An object of class
dendrogram which describes the tree
produced by the clustering algorithm
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